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:2
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Sprint:Summer 3, Summer 4
Description
For this task, create RNA-Seq alignments files (BAM), junction files (bed.gz), and scaled coverage graphs (bedgraph.gz) for data set SRP484252, submitted to Sequence Read Archive by Goldstein Lab at UNC Chapel Hill in 2024.
All code will be saved to main branch in this repository - see: https://bitbucket.org/lorainelab/tardigrade/src/main/
Attachments
Issue Links
Activity
Transferring find junctions outputs.
Checked that the files were made, as expected, with:
[aloraine@str-i2 find_junctions]$ pwd /projects/tomato_genome/fnb/dataprocessing/tardigrade/SRP484252/results/star_salmon/find_junctions [aloraine@str-i2 find_junctions]$ ls *FJ* | wc -l 24
Copying files to deployment directory (rsync source) and specifying desired permissions with:
[aloraine@str-i2 find_junctions]$ cp *FJ* ../../../for_quickload/H_exemplaris_Z151_Apr_2017/SRP484252/. [aloraine@str-i2 find_junctions]$ chmod a+r ../../../for_quickload/H_exemplaris_Z151_Apr_2017/SRP484252/* [aloraine@str-i2 find_junctions]$ chmod g+w ../../../for_quickload/H_exemplaris_Z151_Apr_2017/SRP484252/*
Repeated the rsync command and noticed that after that, all the file permissions in the target directory match the source directory. Maybe file permissions only get updated properly when some data get actually transferred?
Proceeding with adding the new data to annots.xml, as described in preceding comment.
- Launched Excel and opened SRA/SRP484252_SraRunTable.txt (selected comma-delimiter option)
- Saved first draft as to tardigrade/Documentation/inputForMakeAnnotsXml as SRP484252_for_AnnotsXml.xlsx
- Also opened SRP450893_for_AnnotsXml.xlsx for reference
- Edited SRP484252_for_AnnotsXml.xlsx by adding new columns to the front the spreadsheet, and a new column "concentration" for sorting; I wanted the samples to be listed in ascending order of Bleomycin concentration. Used formulas in most of the new columns so that SRR codes and the like would get included automatically, without my having to type a bunch of stuff.
- Picked colors and saved the hex codes and the actual color as a fill color in the spreadsheet.
- Edited src/makeAnnotsXml.py by adding the spreadsheet to a function.
- Ran makeAnnotsXml.py. New annots.xml file got written out.
- Committed and pushed all the changes.
- To deploy the new changes to the rnaseq data source host, logged onto the RENCI VM, changed to the directory for Hypsibus, and ran a script there called "update.sh", which copies the latest annots.xml from the tardigrade repository hosted on bitbucket, with:
cd /projects/igbquickload/lorainelab/www/main/htdocs/rnaseq/H_exemplaris_Z151_Apr_2017 ./update.sh
Here is update.sh:
#! /bin/bash
wget --backups=3 https://bitbucket.org/lorainelab/tardigrade/raw/main/ForGenomeBrowsers/quickload/H_exemplaris_Z151_Apr_2017/annots.xml
Confirmed the colors and the coverage graph files were accessible.
Moving to "needs testing"
To test:
- open genome assembly version H_exemplaris_Z151_Apr_2017
- open folder containing SRP484252 in the name
- open read alignments, coverage graphs, and junction files folders
- check that each file can load by selecting each checkbox, zooming in, and clicking Load Data
See example image:
Testing:
Opened genome assembly version H_exemplaris_Z151_Apr_2017, opened folder containing SRP484252, opened each read alignment file, coverage graphs, and junction files folder by selecting each checkbox, zooming in, and clicking Load Data.
All files properly loaded!
Running prefetch jobs with:
in:
/projects/tomato_genome/fnb/dataprocessing/tardigrade/SRP484252/fastq
Confirmed it worked with:
[aloraine@str-i2 fastq]$ cat *.out | grep -c "was downloaded successfully" 12 [aloraine@str-i2 fastq]$ cut -d , -f 1 SRP484252_SraRunTable.txt | grep -v Run | wc -l 12All 12 runs were prefetched correctly.