{"id":769,"date":"2020-11-04T18:00:36","date_gmt":"2020-11-04T17:00:36","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=769"},"modified":"2022-04-06T14:50:07","modified_gmt":"2022-04-06T12:50:07","slug":"trainings-2019-linux-for-dummies-practice","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-2019-linux-for-dummies\/trainings-2019-linux-for-dummies-practice\/","title":{"rendered":"Trainings 2019 &#8211; Linux For Dummies &#8211; Practice"},"content":{"rendered":"<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Hands On Lab Exercises for Linux<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">Christine Tranchant-Dubreuil (christine.tranchant@ird.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">26\/02\/2018<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">19\/03\/2019<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Modified by<\/td>\n<td style=\"text-align: left;\">Gautier Sarah (gautier.sarah@inra.fr)<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Modified by<\/td>\n<td style=\"text-align: left;\">Christine Tranchant (christine.tranchant@ird.fr)<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>Summary<\/h3>\n<p><!-- TOC depthFrom:2 depthTo:2 withLinks:1 updateOnSave:1 orderedList:0 --><\/p>\n<ul>\n<li><a href=\"#preambule\">Preambule: Softwares to install before connecting to a distant linux server <\/a><\/li>\n<li><a href=\"#practice-1\">Practice 1: Transferring files with filezilla <code>sftp<\/code><\/a><\/li>\n<li><a href=\"#practice-2\">Practice 2: Get Connecting on a linux server by <code>ssh<\/code><\/a><\/li>\n<li><a href=\"#practice-3\">Practice 3: First steps : prompt &amp; <code>pwd<\/code>command<\/a><\/li>\n<li><a href=\"#practice-4\">Practice 4: List the files using <code>ls<\/code> command<\/a><\/li>\n<li><a href=\"#practice-5\">Practice 5 : List the files using <code>MARKDOWN_HASH44ba5ca65651b4f36f1927576dd35436MARKDOWN<em>HASH<\/code> command and metacharacter <\/em>*_<\/a><\/li>\n<li><a href=\"#practice-6\">practice-6 : Moving into file system using <code>cd<\/code>and <code>ls<\/code> commands<\/a><\/li>\n<li><a href=\"#practice-7\">practice-7 : Manipulating Files and Folders<\/a><\/li>\n<li><a href=\"#practice-8\">practice-8 : Searching with <code>grep<\/code><\/a><\/li>\n<li><a href=\"#practice-9\">practice-9 : Blast analysis<\/a><\/li>\n<li><a href=\"#practice-10\">Practice-10: Redirecting a command output to a File with <code>&gt;<\/code><\/a><\/li>\n<li><a href=\"#practice-11\">Practice-11: Sending data from one command to another (piping) with <code>|<\/code><\/a><\/li>\n<li><a href=\"#practice-12\">practice-12 : Dealing with VCF files<\/a><\/li>\n<li><a href=\"#practice-13\">practice-13 : Filtering VCF files<\/a><\/li>\n<li><a href=\"#practice-14\">Practice-14 : Getting basic stats<\/a><\/li>\n<li><a href=\"#tips\">Tips<\/a>\n<ul>\n<li><a href=\"#convertFileFormat\">How to convert between Unix and Windows text files?<\/a><\/li>\n<li><a href=\"#readFile\">How to open and read a file through a text editor on a distant linux server?<\/a><\/li>\n<li><a href=\"#help\">Getting Help on any command-line<\/a><\/li>\n<\/ul>\n<\/li>\n<li><a href=\"#links\">Links<\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"preambule\"><\/a><\/p>\n<h3>Preambule<\/h3>\n<h5>Getting connected to a Linux servers from Windows with SSH (Secure Shell) protocol<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Platform<\/th>\n<th style=\"text-align: left;\">Software<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"20%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osWin.png\"\/><\/td>\n<td style=\"text-align: left;\">mobaXterm<\/td>\n<td style=\"text-align: left;\">An enhanced terminal for Windows with an X11 server and a tabbed SSH client<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/mobaxterm.mobatek.net\/\">More<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>Transferring and copying files from your computer to a Linux servers with SFTP (SSH File Transfer Protocol) protocol<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Platform<\/th>\n<th style=\"text-align: left;\">Software<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"10%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osApple.png\"\/> <img decoding=\"async\" width=\"10%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osLinux.png\"\/> <img decoding=\"async\" width=\"10%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/osWin.png\"\/><\/td>\n<td style=\"text-align: left;\"><img decoding=\"async\" width=\"20%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/filezilla.png\"\/> filezilla<\/td>\n<td style=\"text-align: left;\">FTP and SFTP client<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/filezilla-project.org\/download.php?type=client\">Download<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>Viewing and editing files on your computer before transferring on the linux server or directly on the distant server<\/h5>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Type<\/th>\n<th style=\"text-align: left;\">Software<\/th>\n<th style=\"text-align: left;\">url<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">Distant, consol mode<\/td>\n<td style=\"text-align: left;\">nano<\/td>\n<td style=\"text-align: left;\"><a href=\"http:\/\/www.howtogeek.com\/howto\/42980\/\">Tutorial<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Distant, consol mode<\/td>\n<td style=\"text-align: left;\">vi<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.washington.edu\/computing\/unix\/vi.html\">Tutorial<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Distant, graphic mode<\/td>\n<td style=\"text-align: left;\">komodo edit<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/www.activestate.com\/komodo-ide\/downloads\/edit\">Download<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Linux &amp; windows based editor<\/td>\n<td style=\"text-align: left;\">Notepad++<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/notepad-plus-plus.org\/download\/v7.5.5.html\">Download<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<p><a name=\"practice-1\"><\/a><\/p>\n<h3>Practice 1 : Transferring files with filezilla <code>sftp<\/code><\/h3>\n<h5>Download and install FileZilla<\/h5>\n<h5>Open FileZilla and save the cluster adress into the site manager<\/h5>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-filezilla1.png\"\/><\/p>\n<p>In the FileZilla menu, go to <em>File &gt; Site Manager<\/em>. Then go through these 5 steps:<\/p>\n<ol>\n<li>Click <em>New Site<\/em>.<\/li>\n<li>Add a CUSTOM NAME for this site such as IRD_HPC or AGAP_HPC.<\/li>\n<li>Add the HOSTNAME (see table below).<\/li>\n<li>Set the Logon Type to &quot;Normal&quot; and insert your username and password used to connect on the IRD\/CIRAD HPC<\/li>\n<li>Press the &quot;Connect&quot; button.<\/li>\n<\/ol>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Cluster HPC<\/th>\n<th style=\"text-align: left;\">hostname<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">IRD HPC<\/td>\n<td style=\"text-align: left;\">bioinfo-nas.ird.fr<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">AGAP HPC<\/td>\n<td style=\"text-align: left;\">c2-login.cirad.fr<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<h5>Transferring files<\/h5>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-filezilla2.png\"\/><\/p>\n<ol>\n<li>From your computer to the cluster : click and drag an text file item from the left local colum to the right remote column<\/li>\n<li>From the cluster to your computer : click and drag an text file item from he right remote column to the left local column<\/li>\n<\/ol>\n<hr \/>\n<p><a name=\"practice-2\"><\/a><\/p>\n<h3>Practice 2 : Get Connecting on a linux server by <code>ssh<\/code><\/h3>\n<p>In mobaXterm:<\/p>\n<ol>\n<li>Click the session button, then click SSH.\n<ul>\n<li>In the remote host text box, type: HOSTNAME (see table below)<\/li>\n<li>Check the specify username box and enter your user name<\/li>\n<\/ul>\n<\/li>\n<li>In the console, enter the password when prompted.<br \/>\nOnce you are successfully logged in, you will use this console for the rest of the lecture.<\/li>\n<\/ol>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Cluster HPC<\/th>\n<th style=\"text-align: left;\">hostname<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">IRD HPC<\/td>\n<td style=\"text-align: left;\">bioinfo-nas.ird.fr<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">AGAP HPC<\/td>\n<td style=\"text-align: left;\">c2-login.cirad.fr<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<p><a name=\"practice-3\"><\/a><\/p>\n<h3>Practice 3 : First steps : prompt &amp; <code>pwd<\/code><\/h3>\n<ul>\n<li>What is the current\/working directory just by looking the prompt?<\/li>\n<li>Check the name of your working directory with <code>pwd<\/code> command?<\/li>\n<li>On the console, type your 2 first linux commands to get data necessary for the next (we will explain the two commands latter):<\/li>\n<\/ul>\n<pre><code># get the file on the web\nwget http:\/\/sg.ird.fr\/LINUX-TP\/LINUX-TP.tar.gz\n\n# decompress the gzip file\ntar -xzvf LINUX-TP.tar.gz<\/code><\/pre>\n<ul>\n<li>Check through filezilla the content of your home directory on the server now (cf. filetree just below)<\/li>\n<li>Delete through filezilla the file LINUX-TP.tar.gz on the server<\/li>\n<\/ul>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-arbo.png\"\/><\/p>\n<hr \/>\n<p><a name=\"practice-4\"><\/a><\/p>\n<h3>Practice 4 : List the files using <code>ls<\/code> command<\/h3>\n<ul>\n<li>List the content of your home directory<\/li>\n<li>List the content of the directory <code>Fasta<\/code> by using its absolute path in first then its relative path - <code>ls<\/code> command<\/li>\n<li>List the content of the directory <code>Data<\/code> with the <code>ls<\/code>command and the option <code>-R<\/code><\/li>\n<li>List the content of the directory <code>Bank<\/code> with the <code>ls<\/code>command and the option <code>-al<\/code> or <code>-a -l<\/code><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-5\"><\/a><\/p>\n<h3>Practice 5 : List the files using <code>MARKDOWN_HASH44ba5ca65651b4f36f1927576dd35436MARKDOWN<em>HASH<\/code> command and metacharacter <\/em>*_<\/h3>\n<ul>\n<li>List the content of the directory <code>T-coffee<\/code>. Are there only fasta files ? - <code>ls<\/code> command<\/li>\n<li>List only the files starting by sample (in the directory <code>T-coffee<\/code> ) -  <code>MARKDOWN_HASH44ba5ca65651b4f36f1927576dd35436MARKDOWN<em>HASH<\/code> command &amp; <\/em>*_<\/li>\n<li>List only the files with the fasta extension (in the directory <code>T-coffee<\/code> ) -  <code>MARKDOWN_HASH44ba5ca65651b4f36f1927576dd35436MARKDOWN<em>HASH<\/code> command &amp; <\/em>*_<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-6\"><\/a><\/p>\n<h3>Practice 6 : Moving into file system using <code>cd<\/code>and <code>ls<\/code> command<\/h3>\n<ul>\n<li>Go to the directory <code>Script<\/code> and check in the prompt you have changed correctly your working directory (<code>pwd<\/code>).<\/li>\n<li>List the dir content with <code>ls<\/code>.<\/li>\n<li>Go to the <code>Fasta<\/code> directory using <code>..\/<\/code><\/li>\n<li>Go to the <code>Fastq<\/code> directory . From  this directory, and without any change in your working dir, list what's in <code>samBam<\/code> directory<\/li>\n<li>List <code>vcf<\/code>directory using -R option. What is there in this dir ?<\/li>\n<li>Come back to the home directory.<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-7\"><\/a><\/p>\n<h3>Practice 7 : Manipulating Files and Folders<\/h3>\n<p>We will prepare our blast analysis performed after by creating directory and moving files as showing in the image just below :<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-arbo-blast.png\"\/><\/p>\n<ul>\n<li>Create a directory called <code>BlastAnalysis<\/code> with <code>mkdir<\/code>command.<\/li>\n<li>Move <code>transcritsAssembly.fasta<\/code>  into this new directory with <code>mv<\/code> command.<\/li>\n<li>List the content of <code>LINUX-TP<\/code>and <code>BlastAnalysis<\/code> with <code>ls<\/code> command.<\/li>\n<li>Copy <code>AllEst.fasta<\/code> in <code>Bank<\/code> directory with <code>cp<\/code> command.<\/li>\n<li>List the content of <code>LINUX-TP<\/code>and <code>Bank<\/code> directories. What are the differences between mv and cp?<\/li>\n<li>Remove the file <code>AllEst.fasta<\/code> in <code>LINUX-TP<\/code> directory with <code>rm<\/code> command.<\/li>\n<li>Copy the whole directory <code>T-coffee<\/code> with the name <code>T -coffee-copy<\/code>into <code>LINUX-TP<\/code>directory.<\/li>\n<li>After checking the content of <code>LINUX-TP<\/code>directory, remove the directory <code>T-coffee-copy<\/code>. How to remove a directory ?<\/li>\n<li>Remove all the files into the directory  <code>T-coffee-copy<\/code> with <code>rm *<\/code> command.<\/li>\n<li>Remove the directory <code>T-coffee-copy<\/code>.<\/li>\n<\/ul>\n<p><a name=\"practice-8\"><\/a><\/p>\n<h3>Practice 8 : Searching with <code>grep<\/code><\/h3>\n<ul>\n<li>Go on the following page : <a href=\"http:\/\/rice.plantbiology.msu.edu\/pub\/data\/Eukaryotic_Projects\/o_sativa\/annotation_dbs\/pseudomolecules\/version_7.0\/\">http:\/\/rice.plantbiology.msu.edu\/pub\/data\/Eukaryotic_Projects\/o_sativa\/annotation_dbs\/pseudomolecules\/version_7.0\/<\/a><\/li>\n<li>Copy the url of the rice genome annotation file (gff format) that we will use to download the file directly on the server<\/li>\n<li>Go to the <code>bank<\/code>directory and type the following command :<\/li>\n<\/ul>\n<pre><code>wget gff_url<\/code><\/pre>\n<ul>\n<li>After checking the content of your current directory, what have you done with the <code>$wget<\/code>command?<\/li>\n<li>Displays the firsts and lasts lines of the gff file<\/li>\n<li>Prints the number of lines with the word genes in the gff file<\/li>\n<li>Counts the number of genes<\/li>\n<li>Searchs for the nbs-lrr genes<\/li>\n<li>Removes the lines with putative word<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-9\"><\/a><\/p>\n<h3>Practice 9 : Blast analysis<\/h3>\n<h5>Creating a custom database with <code>makeblastdb<\/code><\/h5>\n<p>As we use a custom database for the first time, If we have a fasta format file of these sequences we have to create a database from our fasta format file <code>AllEst.fasta<\/code> with the <code>makeblastdb<\/code> command.<\/p>\n<ul>\n<li>\n<p>Go into the <code>bank<\/code> directory and create a nucleotide database by typing:<\/p>\n<pre><code>module load bioinfo\/ncbi-blast\/2.6.0\nmakeblastdb -in AllEst.fasta -dbtype nucl -parse_seqids<\/code><\/pre>\n<\/li>\n<li>\n<p>List the content of the directory to check if the database has been indexed<\/p>\n<\/li>\n<\/ul>\n<h5>BLASTing against our remote database<\/h5>\n<ul>\n<li>Go into the <code>blastAnalysis<\/code> directory<\/li>\n<li>Run the blast by typing the following command with the outfmt equals to 6 :<\/li>\n<\/ul>\n<pre><code>blastn \u2013query fastaFile -db databaseFile \u2013outfmt [0-11]  -out resultFile<\/code><\/pre>\n<ul>\n<li>Output formats<\/li>\n<\/ul>\n<pre><code>The flag for the output format is -outfmt followed by a number which denotes the format request :\n\n0 = pairwise,\n1 = query-anchored showing identities,\n2 = query-anchored no identities,\n3 = flat query-anchored, show identities,\n4 = flat query-anchored, no identities,\n5 = XML Blast output,\n6 = tabular,\n7 = tabular with comment lines,\n8 = Text ASN.1,\n9 = Binary ASN.1,\n10 = Comma-separated values,\n11 = BLAST archive format (ASN.1)\n&lt;\/pre&gt;<\/code><\/pre>\n<ul>\n<li>Output tabular format (6 or 7): one line per results splitted in 12 fields.<\/li>\n<\/ul>\n<pre><code>1. query id\n2. subject id\n3. percent identity\n4. alignment length\n5. number of mismatche-\n6. number of gap openings\n7. query start\n8. query end\n9. subject start\n10. subject end\n11. expect value\n12. bit score<\/code><\/pre>\n<h5>Parsing the results file<\/h5>\n<ul>\n<li>Display  the  first  10  lines  of  the  file  - <code>head<\/code><\/li>\n<li>Display  the  first  15  lines  of  the  file  - <code>head<\/code><\/li>\n<li>Display  it  last  15  lines  - <code>tail<\/code><\/li>\n<li>Count  the  number  of  line - <code>wc<\/code><\/li>\n<li>Sort the lines using the second field (subject  id) by alphabetical order, ascending then descending   - <code>sort<\/code><\/li>\n<li>Sort lines by e\u2010value (ascending) and by \u201calignment length\u201d (descending) - <code>sort<\/code><\/li>\n<li>Extract the first 4 fields - <code>cut<\/code><\/li>\n<li>Extract query id, subject id, evalue, alignment length <code>cut<\/code><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-10\"><\/a><\/p>\n<h3>Practice 11 : Redirecting a command output to a File with <code>&gt;<\/code><\/h3>\n<ul>\n<li>Extract all ESTs identifiers and print them in the file  ESTs_accession.list - <code>cut &gt;<\/code><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-11\"><\/a><\/p>\n<h3>Practice 12 :  Sending data from one command to another (piping) with <code>|<\/code><\/h3>\n<ul>\n<li>How many sequences have a homology with EST sequences ? (TIPs: <code>cut<\/code> command with <code>sort -u<\/code> (uniq) or <code>uniq<\/code> command ))<\/li>\n<li>Extract ESTs sequences from database with <code>blastdbcmd<\/code> by typing :<\/li>\n<\/ul>\n<pre><code>blastdbcmd -entry_batch hits.txt -db bank -out hits.fasta <\/code><\/pre>\n<pre><code> -entry_batch is the file containing the sequence names <\/code><\/pre>\n<ul>\n<li>Count the number of sequences extracted - <code>grep &quot;&gt;&quot; c <\/code><\/li>\n<li>Get the help of <code>infoseq<\/code> program - <code>infoseq --h<\/code><\/li>\n<li>Run infoseq program on your fasta file created just before\n<pre><code>infoseq -sequence FASTA_FILE | head<\/code><\/pre>\n<\/li>\n<li>Display only accession, length and pgc column either with cut command or directly with infosee<\/li>\n<li>What is the shorthest sequence (Accession and length)?<\/li>\n<li>What is the longuest sequence (Accession and length)?<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-12\"><\/a><\/p>\n<h3>Practice 12 : Dealing with vcf Files<\/h3>\n<ul>\n<li>List the content of the directory <code>\/scratch\/VCF_LINUX<\/code><\/li>\n<li>Before creating your directory <code>\/scratch\/VCF_LINUX_FORMATIONX<\/code>, displays the amount of disk space available on the file system with the command <code>df<\/code><\/li>\n<li>Create your directory the directory <code>\/scratch\/VCF_LINUX_FORMATIONX<\/code>and go into it.<\/li>\n<li>Create a shortcut of the different vcf file in the directory <code>\/scratch\/VCF_LINUX<\/code>  with the command <code>ln -s source_file myfile<\/code><\/li>\n<\/ul>\n<p>For example<\/p>\n<pre><code>ln -s \/scratch\/VCF_LINUX_FORMATIONX\/OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION.vcf OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION.LINK.vcf<\/code><\/pre>\n<p>Thus, OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION.LINK.vcf is the name of the new file containing the reference to the file named OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION.vcf.<\/p>\n<ul>\n<li>Repeat the same operation with the other vcf files<\/li>\n<li>List the content of the directory <code>VCF_LINUX_FORMATIONX<\/code> with <code>ls -l<\/code><\/li>\n<li>Display the size of each vcf files in the directory <code>\/scratch\/VCF_LINUX<\/code> then in your directory <code>\/scratch\/VCF_LINUX_FORMATIONX<\/code> - <code>du<\/code><\/li>\n<li>Display the size of the directory <code>\/scratch\/VCF_LINUX<\/code> and the directory <code>\/scratch\/VCF_LINUX_FORMATIONX<\/code> - <code>du<\/code><\/li>\n<li>Displays the first lines of the vcf files - <code>head<\/code>command<\/li>\n<li>Displays the last lines of the vcf files - <code>tail<\/code> command<\/li>\n<li>Count the lines of the vcf files - <code>wc -l<\/code> command<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-13\"><\/a><\/p>\n<h3>Practice 13 :  Filtering VCF files <code>|<\/code> - <code>grep<\/code><\/h3>\n<p>To get some basics stats of the output VCF files, let's use linux command!<\/p>\n<ul>\n<li>How many polymorphisms were detected (Displaying all the lines which does not start with # \/ header lines) in the different vcf files ?<\/li>\n<li>How many polymorphisms were considered &quot;good&quot; after filtering steps by GATK VARIANTFILTRATION (ie marked <code>PASS<\/code>)?<\/li>\n<li>How many polyporphisms were considered &quot;bad&quot; and filtered out (Displaying all the lines without the <code>PASS<\/code> tag )?<\/li>\n<li>Save only the &quot;good&quot; polymorphisms detected that were considered &quot;good&quot; in a new file called <code>OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION.GOOD.vcf<\/code><\/li>\n<li>Display the size of this new vcf files<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-14\"><\/a><\/p>\n<h3>Practice 14 : Getting basic stats<\/h3>\n<ul>\n<li>Go into the directory <code>LINUX-TP\/Data\/fastq\/pairedTwoIndividusGzippedIrigin<\/code> - <code>cd<\/code><\/li>\n<li>List the directory content<\/li>\n<li>Run fastq-stats program ( <a href=\"http:\/\/manpages.ubuntu.com\/manpages\/xenial\/man1\/fastq-stats.1.html\">more<\/a> to get stats about the fastq file <code>irigin1_1.fastq.gz<\/code>\n<pre><code>fastq-stats -D irigin1_1.fastq.gz<\/code><\/pre>\n<\/li>\n<li>BONUS :<br \/>\nUse a <code>for<\/code> loop to run fastq-stats with every fastq file in the directory<\/p>\n<pre><code>for file in *fastq; do \nfastq-stats -D $file &gt; $file.fastq-stats ; \ndone;<\/code><\/pre>\n<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"tips\"><\/a><\/p>\n<h3>Tips<\/h3>\n<p><a name=\"convertFileFormat\"><\/a><\/p>\n<h5>How to convert between Unix and Windows text files?<\/h5>\n<p>The format of Windows and Unix text files differs slightly. In Windows, lines end with both the line feed and carriage return ASCII characters, but Unix uses only a line feed. As a consequence, some Windows applications will not show the line breaks in Unix-format files. Likewise, Unix programs may display the carriage returns in Windows text files with Ctrl-m (^M) characters at the end of each line.<\/p>\n<p>There are many ways to solve this problem as using text file compatible, unix2dos \/ dos2unix command or vi to do the conversion. To use the two last ones, the files to convert must be on a Linux computer.<\/p>\n<h6>use notepad as file editor on windows<\/h6>\n<p>When using Unix files on Windows, it is useful to convert the line endings to display text files correclty in other Windows-based or linux-based editors.<\/p>\n<p>In Notepad++: <code>Edit &gt; EOL Conversion &gt; Windows Format<\/code><\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-notepadUTF8.png\"\/><\/p>\n<h6><code>unix2dos<\/code> &amp; <code>dos2unix<\/code><\/h6>\n<pre><code>\n# Checking if my fileformat is dos\n[tranchant@master0 ~]$ cat -v test.txt\njeidjzdjzd^M\ndjzoidjzedjzed^M\nndzndioezdnezd^M\n\n# Converting from dos to linux format\n[tranchant@master0 ~]$ dos2unix test.txt\ndos2unix: converting file test.txt to Unix format ...\n[tranchant@master0 ~]$ cat -v test.txt\njeidjzdjzd\ndjzoidjzedjzed\nndzndioezdnezd\n\n# Converting from linux to dos format\n[tranchant@master0 ~]$ unix2dos test.txt\nunix2dos: converting file test.txt to DOS format ...\n[tranchant@master0 ~]$ cat -v test.txt\njeidjzdjzd^M\ndjzoidjzedjzed^M\nndzndioezdnezd^M\n[tranchant@master0 ~]$\n<\/code><\/pre>\n<h6>vi<\/h6>\n<ul>\n<li>In vi, you can remove carriage return <em>^M <\/em> characters with the following command: <code>:1,$s\/^M\/\/g<\/code><\/li>\n<li>To input the <em>^M<\/em> character, press <em>Ctrl-v<\/em>, and then press <em>Enter<\/em> or <em>return<\/em>.<\/li>\n<li>In vim, use :<code>set ff=unix<\/code> to convert to Unix; use <code>:set ff=dos<\/code> to convert to Windows.<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"readFile\"><\/a><\/p>\n<h5>How to open and read a file through a text editor on a distant linux server?<\/h5>\n<h6>vi<\/h6>\n<p><a href=\"https:\/\/www.washington.edu\/computing\/unix\/vi.html\/\">Manual<\/a><\/p>\n<h6>nano<\/h6>\n<p><a href=\"https:\/\/www.howtogeek.com\/howto\/42980\/\">Manual<\/a><\/p>\n<h6>Komodo Edit<\/h6>\n<p>After installing Komodo Edit, open it and click on <em>Edit \u2013&gt; Preferences<\/em><\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-komodoEdit1.png\"\/><\/p>\n<p>Select Servers from the left and enter sftp account information, then save it.<\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-komodoEdit2.png\"\/><\/p>\n<p>To edit a distant content, click on <em>File \u2013&gt; Open \u2013&gt; Remote File<\/em><\/p>\n<p><img decoding=\"async\" width=\"100%\" class=\"img-responsive\" src=\"https:\/\/southgreenplatform.github.io\/trainings\/\/images\/tpLinux\/tp-komodoEdit3.png\"\/><\/p>\n<hr \/>\n<p><a name=\"help\"><\/a><\/p>\n<h4>Getting Help on any command-line<\/h4>\n<h6>with the option <code>--help<\/code><\/h6>\n<p>Virtually all commands understand the <code>-h<\/code> (or <code>--help<\/code>) option, which produces a short usage description of the command and its options.<\/p>\n<pre>\n<code>\n[tranchant@master0 ~]$ ls --help\nUtilisation : ls [OPTION]... [FILE]...\nAfficher des renseignements sur les FILEs (du r\u00e9pertoire actuel par d\u00e9faut).\nTrier les entr\u00e9es alphab\u00e9tiquement si aucune des options -cftuvSUX ou --sort\nne sont utilis\u00e9es.\n\nLes arguments obligatoires pour les options longues le sont aussi pour les\noptions courtes.\n  -a, --all                  ne pas ignorer les entr\u00e9es d\u00e9butant par .\n  -A, --almost-all           ne pas inclure . ou .. dans la liste\n      --author               avec -l, afficher l'auteur de chaque fichier\n  -b, --escape               afficher les caract\u00e8res non graphiques avec des\n                               protections selon le style C\n      --block-size=SIZE      convertir les tailles en SIZE avant de les\n                               afficher. Par exemple, \u00ab --block-size=M \u00bb affiche\n                               les tailles en unit\u00e9s de 1 048 576 octets ;\n                               consultez le format SIZE ci-dessous\n  -B, --ignore-backups       ne pas inclure les entr\u00e9es se terminant par ~ dans\n                               la liste\n  -c                         avec -lt : afficher et trier selon ctime (date de\n                               derni\u00e8re modification provenant des informations\n                               d'\u00e9tat du fichier) ;\n                               avec -l : afficher ctime et trier selon le nom ;\n                               autrement : trier selon ctime\n  -C                         afficher les noms en colonnes\n      --color[=WHEN]         colorier la sortie ; par d\u00e9faut, WHEN peut \u00eatre\n                               \u00ab never \u00bb (jamais), \u00ab auto \u00bb (automatique) ou\n                               \u00ab always \u00bb (toujours, valeur par d\u00e9faut) ; des\n                               renseignements compl\u00e9mentaires sont ci-dessous\n  -d, --directory            afficher les noms de r\u00e9pertoires, pas leur contenu\n...\n\n<\/code>\n<\/pre>\n<h6>with the <code>man<\/code> command<\/h6>\n<p>Every command and nearly every application in Linux has a man (manual) file, so finding such a file is as simple as typing man command to bring up a longer manual entry for the specified command.<\/p>\n<pre>\n<code>\n# Type man ls to display the related manual\n\nLS(1)                                      Manuel de l'utilisateur Linux                                      LS(1)\n\nNOM\n       ls, dir, vdir - Afficher le contenu d'un r\u00e9pertoire\n\nSYNOPSIS\n       ls [options] [fichier...]\n       dir [fichier...]\n       vdir [fichier...]\n\n       Options POSIX : [-CFRacdilqrtu1] [--]\n\n       Options  GNU  (forme  courte)  :  [-1abcdfgiklmnopqrstuvwxABCDFGHLNQRSUX]  [-w  cols]  [-T  cols] [-I motif]\n       [--full-time]  [--show-control-chars]   [--block-size=taille]   [--format={long,verbose,commas,across,verti\u2010\n       cal,single-column}]       [--sort={none,time,size,extension}]       [--time={atime,access,use,ctime,status}]\n       [--color[={none,auto,always}]] [--help] [--version] [--]\n\nDESCRIPTION\n       La commande ls affiche tout d'abord l'ensemble de ses arguments fichiers autres que des r\u00e9pertoires. Puis ls\n       affiche  l'ensemble  des  fichiers  contenus  dans chaque r\u00e9pertoire indiqu\u00e9. Si aucun argument autre qu'une\n       option n'est fourni, l'argument \u00ab . \u00bb (r\u00e9pertoire en cours) est pris  par  d\u00e9faut.  Avec  l'option  -d,  les\n       r\u00e9pertoires  fournis  en argument ne sont pas consid\u00e9r\u00e9s comme des r\u00e9pertoires (on affiche leurs noms et pas\n       leurs contenus). Un fichier n'est affich\u00e9 que si son nom ne commence pas par un point, ou si l'option -a est\n       fournie.\n\n       Chacune  des  listes  de fichiers (fichiers autres que des r\u00e9pertoires, et contenu de chaque r\u00e9pertoire) est\n       tri\u00e9e s\u00e9par\u00e9ment en fonction de la s\u00e9quence d'ordre de la localisation en cours.  Lorsque  l'option  -l  est\n       .....\n<\/code>\n<\/pre>\n<p>Some helpful tips for using the man command :<\/p>\n<ul>\n<li><code>Arrow keys<\/code>: Move up and down the man file by using the arrow keys.<\/li>\n<li><code>q<\/code>: Quit back to the command prompt by typing q.<\/li>\n<\/ul>\n<hr \/>\n<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li>Related courses : <a href=\"https:\/\/southgreenplatform.github.io\/trainings\/linux\/\">Linux for Dummies<\/a><\/li>\n<li>Tutorials : <a href=\"https:\/\/southgreenplatform.github.io\/trainings\/linux\/linuxTuto\/\">Linux Command-Line Cheat Sheet<\/a><\/li>\n<\/ul>\n<hr \/>\n<h3>License<\/h3>\n<p><a name=\"license\"><\/a><\/p>\n<div>\nThe resource material is licensed under the Creative Commons Attribution 4.0 International License (<a href=\"http:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/\">here<\/a>).<br \/>\n<center><img decoding=\"async\" width=\"25%\" class=\"img-responsive\" src=\"http:\/\/creativecommons.org.nz\/wp-content\/uploads\/2012\/05\/by-nc-sa1.png\"\/><br \/>\n<\/center>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>Description Hands On Lab Exercises for Linux Authors Christine Tranchant-Dubreuil (christine.tranchant@ird.fr) Creation Date 26\/02\/2018 Last Modified Date 19\/03\/2019 Modified by&hellip; 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