{"id":763,"date":"2020-11-04T17:57:50","date_gmt":"2020-11-04T16:57:50","guid":{"rendered":"https:\/\/itrop.ird.fr\/wordpress\/?page_id=763"},"modified":"2022-04-06T14:50:07","modified_gmt":"2022-04-06T12:50:07","slug":"trainings-linux-for-jedi-practice","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/trainings-fr\/trainings-linux-for-jedi\/trainings-linux-for-jedi-practice\/","title":{"rendered":"Trainings 2019 &#8211; Linux for Jedi &#8211; Practice"},"content":{"rendered":"<h2>Advanced Linux Practice page<\/h2>\n<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;\">Related-course materials<\/td>\n<td style=\"text-align: left;\"><a href=\"https:\/\/southgreenplatform.github.io\/trainings\/linux\/linuxPracticeJedi\/\/\">Linux for Jedi<\/a><\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Authors<\/td>\n<td style=\"text-align: left;\">Christine Tranchant-Dubreuil (christine.tranchant@ird.fr) &amp; Gautier Sarah (gautier.sarah<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">11\/03\/2018<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">14\/04\/2019<\/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>\n<p><a href=\"#preambule\">Preambule: Softwares to install before connecting to a distant linux server <\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-1\">Practice 1: Get Connecting on a linux server by <code>ssh<\/code><\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-2\">Practice 2: Preparing working environnement<\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-3\">Practice 3: Monitoring processes) with <code>w, ps, kill, top<\/code><\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-4\">Practice 4: Using the <code>&amp;&amp;<\/code> separator<\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-5\">Practice 5: Searching for text using <code>grep<\/code><\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-6\">Practice 6: Displaying lines with <code>sed<\/code><\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-7\">Practice 7: Deleting lines with <code>sed<\/code><\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-8\">Practice 8: Parsing files with <code>sed<\/code> using regexp<\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-9\">Practice 9: Modifying files with <code>sed<\/code><\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#practice-10\">Practice 10: Manipulating files with <code>awk<\/code><\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#links\">Links<\/a><\/p>\n<\/li>\n<li>\n<p><a href=\"#license\">License<\/a><\/p>\n<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"preambule\"><\/a><\/p>\n<h3>Preambule<\/h3>\n<ul>\n<li>List of Softwares to install before connecting to a distant linux server <a href=\"https:\/\/southgreenplatform.github.io\/trainings\/linux\/linuxPractice\/#preambule\">more information<\/a><\/li>\n<li>Arborescence image :<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-1\"><\/a><\/p>\n<h3>Practice 1 : 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-master.ird.fr<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">AGAP HPC<\/td>\n<td style=\"text-align: left;\">cc2-login.cirad.fr<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<ul>\n<li>Connect on the HPC<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-2\"><\/a><\/p>\n<h3>Practice 2 : Preparing working environnement<\/h3>\n<ul>\n<li>Type qrsh to connect on one node<\/li>\n<li>Move into the directory \/scratch<\/li>\n<li>Create a working directory such as Formation-X (X corresponds to your login id\/number) <\/li>\n<li>Move into this directory just created and check the current\/working directory just by looking the prompt<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-3\"><\/a><\/p>\n<h3>Practice 3 :  Monitoring processes<\/h3>\n<h4>Displaying the list of processes<\/h4>\n<ul>\n<li>Type the command <code>w<\/code> through 2 consoles : one connected on bioinfo-master, the other connected on one node<\/li>\n<li>Type (on the node) the command <code>ps<\/code>without option, then with the option <code>u<\/code>, <code>ua<\/code>,  <code>uax<\/code><\/li>\n<li>Type the command <code>top<\/code>on the node <\/li>\n<li>Then use the &quot;option&quot; c to display the complete process<\/li>\n<li>Then use the &quot;option&quot; u to display only your processes<\/li>\n<\/ul>\n<h4>Kill a process - downloading files from SRA through two ways<\/h4>\n<p>We want to download one fastq file from NCBI SRA (available here <a href=\"https:\/\/trace.ncbi.nlm.nih.gov\/Traces\/sra\/?run=SRR304976\">https:\/\/trace.ncbi.nlm.nih.gov\/Traces\/sra\/?run=SRR304976<\/a> ) using SRAtoolkit as below :<\/p>\n<p><code>module load sratoolkit fastq-dump SRRXXXX<\/code><\/p>\n<p>This will download the SRA file (in sra format) and then convert them to fastq file for you. More details on <a href=\"https:\/\/isugenomics.github.io\/bioinformatics-workbook\/dataAcquisition\/fileTransfer\/sra.html\">https:\/\/isugenomics.github.io\/bioinformatics-workbook\/dataAcquisition\/fileTransfer\/sra.html<\/a><\/p>\n<ul>\n<li>Download the fastq file in the directory created precedently in \/scratch<\/li>\n<li>Open a new terminal to connect on bioinfo-master.ird.fr <\/li>\n<li>From this terminal, display the list of processes running on the node where you are downloading the fastq file with fastq-dump<\/li>\n<li>From this terminal, kill your process &quot;fastq-dump&quot; directly from bioinfo-master<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-4\"><\/a><\/p>\n<h3>Practice 4 : Using the &amp;&amp; separator<\/h3>\n<ul>\n<li>On the console, type the 2 following 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 and decompress the gzip file \nwget http:\/\/sg.ird.fr\/LINUX-TP\/LINUX-TP.tar.gz &amp;&amp; tar -xzvf LINUX-TP.tar.gz\n<\/code><\/pre>\n<ul>\n<li>Check the content of your home directory on the server now (cf. filetree just below)<\/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-5\"><\/a><\/p>\n<h3>Practice 5 : Searching for text using <code>grep<\/code><\/h3>\n<h4>from a gff file<\/h4>\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>Prints the number of lines with the word <code>gene<\/code> in the gff file - <code>grep -P<\/code><\/li>\n<li>Counts the number of genes - <code>grep -c<\/code> <\/li>\n<li>Search for the nbs-lrr genes - <code>grep -i<\/code><\/li>\n<li>Removes the lines with <code>putative<\/code> word - <code>grep -v<\/code><\/li>\n<li>Counts the number of mRNA in the chromosome 1 - <code>grep -c regexp<\/code><\/li>\n<li>Counts the number of mRNA in the first five chromosomes - <code>grep -c regexp<\/code><\/li>\n<\/ul>\n<h4>from a fasta file<\/h4>\n<ul>\n<li>Get from the same website the cDNA sequences of the rice genome (fasta format) <code>wget<\/code><\/li>\n<li>Get the help of <code>infoseq<\/code> program - <code>infoseq --h<\/code><\/li>\n<li>Run infoseq program on the fasta file just downloaded\n<pre><code>infoseq -sequence FASTA_FILE | head<\/code><\/pre>\n<\/li>\n<li>Display only accession, length and pgc column with the options of <code>infoseq<\/code><\/li>\n<li>What is the shorthest sequence (Accession and length)? <code>infoseq, sort, head<\/code><\/li>\n<li>What is the longuest sequence (Accession and length)? <code>infoseq, sort, head<\/code><\/li>\n<li>Count the number of sequences with a length between 1000 and 9999 with <code>grep<\/code><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-6\"><\/a><\/p>\n<h3>Practice 6 :  Displaying lines with <code>sed<\/code><\/h3>\n<p>For this exercise, you will work on the fastq file LINUX-TP\/Data\/fastq\/pairedTwoIndividusGzippedIrigin\/irigin1_1.fastq.gz<\/p>\n<ul>\n<li>Print the 8 first lines<\/li>\n<li>Print the lines 5 to 12<\/li>\n<li>Print only the sequences ids<\/li>\n<li>Print only the sequences ids and nucleotides sequences<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-7\"><\/a><\/p>\n<h3>Practice 7 : Deleting lines with <code>sed<\/code><\/h3>\n<p>For this exercise, you will work on the fastq file LINUX-TP\/Data\/fastq\/pairedTwoIndividusIrigin\/irigin1_1.fastq<\/p>\n<ul>\n<li>Delete the end of the file from the line 9<\/li>\n<li>Delete the lines containing only a <code>+<\/code><\/li>\n<li>Delete the lines containing only a <code>+<\/code> and the quality sequences<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-8\"><\/a><\/p>\n<h3>Practice 8 : File parsing with <code>sed<\/code> using regexp<\/h3>\n<h4>From the gff file precedently downloaded<\/h4>\n<ul>\n<li>Count the number of genes<\/li>\n<\/ul>\n<h4>From a vcf file<\/h4>\n<ul>\n<li>Download the vcf file available at this url <a href=\"http:\/\/sg.ird.fr\/LINUX-TP\/OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION-100000.vcf.tar.gz\">http:\/\/sg.ird.fr\/LINUX-TP\/OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION-100000.vcf.tar.gz<\/a><\/li>\n<li>How many polymorphisms were considered bad and filtered out (Displaying all the lines without neither the <code>PASS<\/code> tag nor starting with <code>#<\/code> )?<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-9\"><\/a><\/p>\n<h3>Practice 9 : File modification with <code>sed<\/code><\/h3>\n<h4>From the vcf file OgOb-all-MSU7-CHR6.GATKVARIANTFILTRATION-100000.vcf<\/h4>\n<ul>\n<li>Transform the vcf file in a coordinate file <code>chr\\tpos\\tpos<\/code><\/li>\n<li>Now, in the VCF file, we would like to replace the genotypes by allelic dose. This means that we should replace the whole field by <code>0<\/code> when the genotype is <code>0\/0<\/code>, by <code>1<\/code> when the genotype is <code>0\/1<\/code> and <code>2<\/code> when the genotype is <code>1\/1<\/code><\/li>\n<\/ul>\n<h4>From fasta files in <code>LINUX-TP\/Fasta<\/code><\/h4>\n<ul>\n<li>In <code>fasta<\/code> directory, there are two files : <code>C_AllContigs.fasta<\/code> and <code>contig_tgicl.fasta<\/code>. Before to generate a unique file with all 2 libraries, we would like to tag each sequence per its origin. In each file, add the respective tag VS1- \/ VS2- just before the identifier.<\/li>\n<\/ul>\n<pre><code># File C_AllContigs.fasta initially\n>C_pseu_c1\nAAAAATGTTTGAAATCCACTTGGCATTMAATGGTGAAAGAATTTTAGATTTTTATATACT\nCCCTCGGTAAGGAAATTGTTGTCTCATTTTGGGATTCACAATTATTACCAACAGTGCAAG\nGGTTTT\n\n#File C_AllContigs.fasta\n>VS1-C_pseu_c1\nAAAAATGTTTGAAATCCACTTGGCATTMAATGGTGAAAGAATTTTAGATTTTTATATACT\nCCCTCGGTAAGGAAATTGTTGTCTCATTTTGGGATTCACAATTATTACCAACAGTGCAAG\nGGTTTT<\/code><\/pre>\n<p>Rq : Test first the sed command on one file and STDOUT, then store the results in new files named RN-VS.MID1.clean.sff.fasta \u2026<\/p>\n<ul>\n<li>Generate a file named all-contigs.fasta with all the sequences - <code>cat file1 file2 &gt; file3<\/code><\/li>\n<li>Count the number of sequences in the fasta file just created <code>grep -c &quot;&gt;&quot; <\/code><\/li>\n<li>Count the sequence number of each library in this file<\/li>\n<\/ul>\n<h4>From fastq files in <code>Data\/fastq\/pairedTwoIndividusIrigin<\/code><\/h4>\n<ul>\n<li>In the directory <code>Data\/fastq\/pairedTwoIndividusIrigin<\/code> transform the fastq file irigin1_1.fastq in fasta format<\/li>\n<li>In one command line transform all fastq files of the directory in fasta (save the files before)<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-10\"><\/a><\/p>\n<h3>Practice 10 : Manipulating files with <code>awk<\/code><\/h3>\n<h4>From the gff file precedently downloaded<\/h4>\n<ul>\n<li>Extract the coordinate from the gff file<\/li>\n<li>Calculate the mean of the gene length<\/li>\n<li>Calculate the mean of the gene length for the chromosome 1<\/li>\n<li>Count the number of genes above 2000bp length<\/li>\n<li>Bonus: calculate the mean of gene length for each chromosomes in one command line<\/li>\n<\/ul>\n<h4>From the result of a nucmer analysis<\/h4>\n<p>We want to rapidly align an assembly against a entire genome using nucmer. (i.e., assembling etc.) to a reference genome. Type the three following commands :<\/p>\n<pre><code>#So we compare one multifasta that have been created against a genome\nnucmer --mum reference.fasta contigs.fasta -p ctgVSref.NUCMER\n\n#The previous command produces a file named ctgVSref.NUCMER.delta that can then be filtered using delta-filter and formatted using show-coords to produce a human-readable table of overlapping alignments between the two multifastas.\n\n#Filtering the nucmer results \n#The -l in delta-filter sets the minimum alignment length to 300. The -q \u201cMaps each position of each query to its best hit in the reference, allowing for reference overlaps\u201d.\ndelta-filter -l300 -q ctgVSref.NUCMER.delta &gt; ctgVSref.filter300.delta\n\n#Generate results (tab format)\n#The -c and -l in show-coords indicate that percent identity and sequence length information, respectively, should be included in the output. -L sets the minimum alignment length to display, -r sorts the output lines by reference IDs and coordinates, and -T switches the output to tab-delimited format.\nshow-coords -c -l -L 300 -r -T ctgOMAP.filter300.delta &gt; ctgOMAP.filter300.delta.coords.txt<\/code><\/pre>\n<ul>\n<li>Count the number of contigs in the fasta file<\/li>\n<li>Count the number of alignements performed by nucmer<\/li>\n<li>Count the number of contigs that have been aligned<\/li>\n<li>sort by alignment percent ascending<\/li>\n<li>count the number of alignement with alignment % &gt; 50 then 80<\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"practice-11\"><\/a><\/p>\n<h3>Practice 11<\/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>Use a <code>for<\/code> loop to run fastq-stats with every fastq file in the directory\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<h3>Links<\/h3>\n<p><a name=\"links\"><\/a><\/p>\n<ul>\n<li>Related courses : <a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/trainings-2019-linux-for-dummies\/\">Linux for Jedi<\/a><\/li>\n<li>Tutorials : <a href=\"https:\/\/itrop.ird.fr\/wordpress\/index.php\/linux-tutorial\/\">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>Advanced Linux Practice page Description Hands On Lab Exercises for Linux Related-course materials Linux for Jedi Authors Christine Tranchant-Dubreuil (christine.tranchant@ird.fr)&hellip; 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