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  1. IGB
  2. IGBF-3042

Get RNA-Seq data from SRA

        Details

        • Type: Task
        • Status: Closed (View Workflow)
        • Priority: Major
        • Resolution: Done
        • Affects Version/s: None
        • Fix Version/s: None
        • Labels:
          None

          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

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              relates to

              Task - A task that needs to be done. IGBF-3040 Create samplesheet with SRR run identifiers and experimental attributes

              • Major - Major loss of function.
              • Closed

                Activity

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                ann.loraine Ann Loraine created issue -
                ann.loraine Ann Loraine made changes -
                Field Original Value New Value
                Epic Link IGBF-3039 [ 21553 ]
                ann.loraine Ann Loraine made changes -
                Sprint Spring 2 2022 Jan 18 - Jan 28 [ 137 ] Spring 1 2022 Jan 3 - Jan 14 [ 136 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked lower
                ann.loraine Ann Loraine made changes -
                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.

                Put script under version-control in:

                * salty_rice/bseq_rice/src                 		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
                ann.loraine Ann Loraine made changes -
                Link This issue relates to IGBF-3040 [ IGBF-3040 ]
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                ann.loraine Ann Loraine added a comment -

                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.

                Show
                ann.loraine Ann Loraine added a comment - 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.
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                ann.loraine Ann Loraine made changes -
                Assignee Ann Loraine [ aloraine ]
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                ann.loraine Ann Loraine added a comment - - edited

                Downloading and converting the files on the cluster now.

                Show
                ann.loraine Ann Loraine added a comment - - edited Downloading and converting the files on the cluster now.
                Hide
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                ann.loraine Ann Loraine added a comment - - edited

                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
                Show
                ann.loraine Ann Loraine added a comment - - edited 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
                ann.loraine Ann Loraine made changes -
                Sprint Spring 1 2022 Jan 3 - Jan 14 [ 136 ] Spring 1 2022 Jan 3 - Jan 14, Spring 2 2022 Jan 18 - Jan 28 [ 136, 137 ]
                ann.loraine Ann Loraine made changes -
                Rank Ranked higher
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] To-Do [ 10305 ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                Script added to repository: rnaseq-fasterq-dump.sh.

                Show
                ann.loraine Ann Loraine added a comment - Script added to repository: rnaseq-fasterq-dump.sh.
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                ann.loraine Ann Loraine added a comment -

                Adding script to compress all the files using cluster nodes.

                Show
                ann.loraine Ann Loraine added a comment - Adding script to compress all the files using cluster nodes.
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                ann.loraine Ann Loraine added a comment -

                Compressed fastq files are here: /nobackup/lorainelab/salty_rice/rna-seq

                Show
                ann.loraine Ann Loraine added a comment - Compressed fastq files are here: /nobackup/lorainelab/salty_rice/rna-seq
                ann.loraine Ann Loraine made changes -
                Status To-Do [ 10305 ] In Progress [ 3 ]
                Hide
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                ann.loraine Ann Loraine added a comment -

                Total size of all gzip'd files: 131 Gb
                Moving to Closed.

                Code added:

                Show
                ann.loraine Ann Loraine added a comment - Total size of all gzip'd files: 131 Gb Moving to Closed. Code added: https://bitbucket.org/lorainelab/bseq_rice/src/master/src/sbatch-doIt.sh https://bitbucket.org/lorainelab/bseq_rice/src/master/src/gzip.sh
                ann.loraine Ann Loraine made changes -
                Status In Progress [ 3 ] Needs 1st Level Review [ 10005 ]
                ann.loraine Ann Loraine made changes -
                Status Needs 1st Level Review [ 10005 ] First Level Review in Progress [ 10301 ]
                ann.loraine Ann Loraine made changes -
                Status First Level Review in Progress [ 10301 ] Ready for Pull Request [ 10304 ]
                ann.loraine Ann Loraine made changes -
                Status Ready for Pull Request [ 10304 ] Pull Request Submitted [ 10101 ]
                ann.loraine Ann Loraine made changes -
                Status Pull Request Submitted [ 10101 ] Reviewing Pull Request [ 10303 ]
                ann.loraine Ann Loraine made changes -
                Status Reviewing Pull Request [ 10303 ] Merged Needs Testing [ 10002 ]
                ann.loraine Ann Loraine made changes -
                Status Merged Needs Testing [ 10002 ] Post-merge Testing In Progress [ 10003 ]
                ann.loraine Ann Loraine made changes -
                Resolution Done [ 10000 ]
                Status Post-merge Testing In Progress [ 10003 ] Closed [ 6 ]

                  People

                  • Assignee:
                    ann.loraine Ann Loraine
                    Reporter:
                    ann.loraine Ann Loraine
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                    Watchers:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: