Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Sprint:Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28
Description
Create and run a script (fasterq-dump-rnaseq.sh) that retrieves RNA-Seq data files from the SRA and converts them to fastq format.
See linked issue for a comment containing a first draft of the script code: IGBF-3040
Put script under version-control in:
- salty_rice/bseq_rice/src
Attachments
Issue Links
- relates to
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- Closed
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Activity
Sample output – not sure what "reads 0-length" means:
concat :|-------------------------------------------------- 100% spots read : 38,726,481 reads read : 77,452,962 reads written : 62,196,161 reads 0-length : 15,256,801 join :|-------------------------------------------------- 100% concat :|-------------------------------------------------- 100% spots read : 47,593,574 reads read : 95,187,148 reads written : 76,499,566 reads 0-length : 18,687,582 join :|-------------------------------------------------- 100% concat :|-------------------------------------------------- 100% spots read : 56,233,927 reads read : 112,467,854 reads written : 56,233,927 reads 0-length : 56,233,927 join :|-------------------------------------------------- 100% concat :|-------------------------------------------------- 100% spots read : 52,074,128 reads read : 104,148,256 reads written : 52,074,128 reads 0-length : 52,074,128 join :|-------------------------------------------------- 100% concat :|-------------------------------------------------- 100% spots read : 39,584,294 reads read : 79,168,588 reads written : 39,584,294 reads 0-length : 39,584,294 join :|-------------------------------------------------- 100% concat :|-------------------------------------------------- 100% spots read : 57,668,415 reads read : 115,336,830 reads written : 89,783,065 reads 0-length : 25,553,765 join :|-------------------------------------------------- 100% concat :|-------------------------------------------------- 100% spots read : 41,998,084 reads read : 83,996,168 reads written : 83,996,168 join :|-------------------------------------------------- 100% concat :|-------------------------------------------------- 100% spots read : 45,085,096 reads read : 90,170,192 reads written : 45,085,096 reads 0-length : 45,085,096
Script added to repository: rnaseq-fasterq-dump.sh.
Adding script to compress all the files using cluster nodes.
Compressed fastq files are here: /nobackup/lorainelab/salty_rice/rna-seq
Total size of all gzip'd files: 131 Gb
Moving to Closed.
Code added:
This script will need to be run on the cluster to retrieve the data we want from the SRA and deploy onto the cluster where we do the next data processing steps.
However, there may be a way to do a "dry run" to check that the script code is correct. If possible, try to do that.