{"id":3575,"date":"2022-02-09T09:15:57","date_gmt":"2022-02-09T08:15:57","guid":{"rendered":"https:\/\/bioinfo.ird.fr\/?page_id=3575"},"modified":"2022-04-06T14:50:28","modified_gmt":"2022-04-06T12:50:28","slug":"tutorials-how-to-manage-my-data-after-an-analysis","status":"publish","type":"page","link":"https:\/\/bioinfo.ird.fr\/index.php\/tutorials-fr\/tutorials-how-to-manage-my-data-after-an-analysis\/","title":{"rendered":"Tutorials &#8211; How to manage my data after an analysis?"},"content":{"rendered":"<h2>How to manage my data after an analysis?<\/h2>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">The size of the NGS files (raw or generated by analysis) can be enormous and often varies from ten to hundreds of gigabytes. The storage space is high and requires significant hardware resources. Compressing NGS data is therefore a natural way to significantly reduce the cost of the storage infrastructure and speed up the analyses.<\/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 and Julie Orjuela - DIADE, IRD<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Creation Date<\/td>\n<td style=\"text-align: left;\">09\/02\/2022<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">Last Modified Date<\/td>\n<td style=\"text-align: left;\">13\/02\/2022<\/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=\"#format\">Some NGS file format<\/a><\/li>\n<li><a href=\"#ngs_file-project\">How to know if I have fastq, sam or vcf files in my project directory ?<\/a><\/li>\n<li><a href=\"#get-filesize\">How to get the size of my files or directories ?<\/a><\/li>\n<li><a href=\"#gz-files\">How to compress a fastq or vcf files ? <\/a><\/li>\n<li><a href=\"#sam2bam\">How to compress a sam files ? <\/a><\/li>\n<li><a href=\"#after-mapping\">After a mapping, which files should I keep ? which files should I remove ? <\/a><\/li>\n<li><a href=\"#license\">License<\/a><\/li>\n<\/ul>\n<hr \/>\n<p><a name=\"format\"><\/a><\/p>\n<h1>Some NGS file format<\/h1>\n<p>Almost all the high-throughput sequencing data you will deal with should mainly have the following formats such as fastq, fq, sam, bam or vcf. <\/p>\n<table>\n<thead>\n<tr>\n<th style=\"text-align: left;\">Format<\/th>\n<th style=\"text-align: left;\">Description<\/th>\n<th style=\"text-align: left;\">Used by<\/th>\n<\/tr>\n<\/thead>\n<tbody>\n<tr>\n<td style=\"text-align: left;\">fastq<\/td>\n<td style=\"text-align: left;\">a text-based format to store a nucleotide sequence and its corresponding quality sequence, generally given by the sequencing providers<\/td>\n<td style=\"text-align: left;\">QC tools, cleaning tools, mapping tools<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">sam<\/td>\n<td style=\"text-align: left;\">a tab-delimited text file that contains sequence alignment  data, generally produced after mapping of fastq sequences to a reference tools (Sequence Alignment\/Map format).<\/td>\n<td style=\"text-align: left;\">samtools<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">bam<\/td>\n<td style=\"text-align: left;\">binary version of a SAM file (saving   storage and faster manipulation)<\/td>\n<td style=\"text-align: left;\">samtools, gatk<\/td>\n<\/tr>\n<tr>\n<td style=\"text-align: left;\">vcf<\/td>\n<td style=\"text-align: left;\">The vcf (Variant Call Format) format is a text format used to describe single nucleotide variants (SNVs) as well as insertions, deletions, and other sequence variations.<\/td>\n<td style=\"text-align: left;\">vcftools, BCFtools<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p><code><code>Don&#039;t forget to compress your large NGS files including VCF, FASTQ, and SAM files.  File compression is a simple method of storing a file that has been reduced in size.<\/code><\/code><\/p>\n<p><a name=\"get-filesize\"><\/a><\/p>\n<h3>How to get the size of my files or directories ?<\/h3>\n<h5>A directory<\/h5>\n<p>You can use the <code>du<\/code> command  (disk usage). To find the size of the specific directory, use the following syntax <code>du -h path2dir<\/code> or <code>du -sh path2dir<\/code>:<\/p>\n<pre><code>nas3$ du -h \/data3\/projects\/riceAnnot\/\n1,1G    \/data3\/projects\/riceAnnot\/abyssContigsFiltered\/Obarthii\n861M    \/data3\/projects\/riceAnnot\/abyssContigsFiltered\/Oglaberrima\n2,0G    \/data3\/projects\/riceAnnot\/abyssContigsFiltered\n...\n16G \/data3\/projects\/riceAnnot\/VCFs\n33G \/data3\/projects\/riceAnnot\/ALLVCFs\/tmp\n38G \/data3\/projects\/riceAnnot\/ALLVCFs\n58G \/data3\/projects\/riceAnnot\/<\/code><\/pre>\n<pre><code>[tranchant@master0 scratch-scripts]$ du -sh\n\/data3\/projects\/riceAnnot\/\n58G \/data3\/projects\/riceAnnot\/<\/code><\/pre>\n<h5>My projects on the cluster<\/h5>\n<p>To list the size of all your projects on nas, nas2 and nas3, use the following script :<\/p>\n<pre><code>nas3$ \/opt\/scripts\/Data\/project.sh \n\n### OWNER - project1 1,5T   \/data\/projects\/project1\n### OWNER - project2 352G   \/data2\/projects\/project2\n\n----------------- Projects as participants\ntoggle\nirigin\n====&gt; TOTAL : 2<\/code><\/pre>\n<p>Be careful : Run this script can be time consuming depending on the number of projects and their size !<\/p>\n<p><a name=\"ngs_file-project\"><\/a><\/p>\n<h3>How to know   if I have fastq, sam or vcf files in my project directory ?<\/h3>\n<p>Use the following script : <code>\/opt\/scripts\/Data\/searchFile.sh path2project extension<\/code><\/p>\n<pre><code>$ \/opt\/scripts\/Data\/searchFile.sh \/data3\/projects\/myproject\/ vcf\n    final_biallelic_random_10perc.vcf\n    final_chr01_C013_C034.recode.vcf\n    Filtered_biallelic.recode.vcf\n    final_chr01.recode.vcf<\/code><\/pre>\n<p><a name=\"gz-files\"><\/a><\/p>\n<h3>How to compress a fastq or vcf files ?<\/h3>\n<h6>List the content of the directory that contains fastq file<\/h6>\n<pre><code>bash-4.2# ls -lh\nSRR453571_1.fastq.gz\n-rwxr-xr-x 1 root formation 541M  4 f\u00e9vr. 13:32 SRR453571_2.fastq.gz\n-rwxr-xr-x 1 root formation 1,3G  4 f\u00e9vr. 13:32 SRR453578_1.fastq.gz\n-rwxr-xr-x 1 root formation 4,9G  4 f\u00e9vr. 13:33 SRR453578_2.fastq<\/code><\/pre>\n<pre><code>bash-4.2# du -h SRR453578_2.fastq\n8,1G    SRR453578_2.fastq<\/code><\/pre>\n<h6>Compress a fastq file with the command <code>gzip -9<\/code><\/h6>\n<pre><code>bash-4.2# du -h SRR453578_2.fastq\n8,1G    SRR453578_2.fastq\n\nbash-4.2#gzip -9  SRR453578_2.fastq\n\nbash-4.2#bash-4.2# ls -lh\ntotal 9,3G\n-rwxr-xr-x 1 root formation 514M  4 f\u00e9vr. 13:32 SRR453571_1.fastq.gz\n-rwxr-xr-x 1 root formation 541M  4 f\u00e9vr. 13:32 SRR453571_2.fastq.gz\n-rwxr-xr-x 1 root formation 1,3G  4 f\u00e9vr. 13:32 SRR453578_1.fastq.gz\n-rwxr-xr-x 1 root formation 1,3G  4 f\u00e9vr. 13:33 SRR453578_2.fastq.gz\n\nbash-4.2# du -h SRR453578_2.fastq.gz\n1,3G    SRR453578_2.fastq.gz\n<\/code><\/pre>\n<h6>How to compress a vcf file ?<\/h6>\n<pre><code>#get vcf size\n$ du -sh ALL.Chr01.F4.GenotypeGVCFS.MQ0.vcf\n7,0G    ALL.Chr01.F4.GenotypeGVCFS.MQ0.vcf\n\n# compress vcf file\n$ gzip -9 ALL.Chr01.F4.GenotypeGVCFS.MQ0.vcf\n\n# get size of the compressed vcf file\n$ du -sh ALL.Chr01.F4.GenotypeGVCFS.MQ0.vcf.gz\n901M    ALL.Chr01.F4.GenotypeGVCFS.MQ0.vcf.gz<\/code><\/pre>\n<p><a name=\"#sam2bam\"><\/a><\/p>\n<h3>How to compress a sam files ?<\/h3>\n<p>SAM format can be compressed in the binary mode BAM by using samtools <a href=\"http:\/\/www.htslib.org\/\">http:\/\/www.htslib.org\/<\/a><\/p>\n<pre><code>samtools view -bh file.sam &gt; file.bam<\/code><\/pre>\n<p>Most tools recognize this format. BAM format allows you to reduce the size of a file by up to 3 times, allowing you gain place in your project.<\/p>\n<p><a name=\"after-mapping\"><\/a><\/p>\n<h3>After a mapping, which files should I keep ? which files should I remove ?<\/h3>\n<p>After mapping you can decide to stock BAM files. In this case, fastq files are not needed.<br \/>\nIt's possible to convert bam files to fastq files. You can do it by using <code>bedtools<\/code> command<br \/>\n<a href=\"https:\/\/bedtools.readthedocs.io\/en\/latest\/content\/tools\/bamtofastq.html\">https:\/\/bedtools.readthedocs.io\/en\/latest\/content\/tools\/bamtofastq.html<\/a>.<\/p>\n<pre><code>bedtools bamtofastq [OPTIONS] -i file.bam -fq fastq<\/code><\/pre>\n<p>In any case, keeping both is redundant !<\/p>\n<p><a name=\"license\"><\/a><\/p>\n<h3>Licence<\/h3>\n<p>The 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>).<\/p>\n<p><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> <\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>How to manage my data after an analysis? 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