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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Epic Link:
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Sprint:Fall 2 2022 Sep 5, Fall 3 2022 Sep 26
Description
Run the arabitag algorithm to tabulate splice junction support using output from find_junctions.sh in linked issue.
Ref: See diagram from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589529/figure/pld3136-fig-0001/
See paper: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589529/
Rice paper repository: https://bitbucket.org/lorainelab/ricealtsplice/src/master/
Arabitag algorithm repository: https://bitbucket.org/lorainelab/altspliceanalysis/src/master/
Attachments
Issue Links
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Activity
Thanks [~molly]. I decided to store all the files in the same folder and will use an index / table of contents type strategy to distinguish them. Moving to Done.
Re-opening to include new work to tabulate results and read into R for interactive analysis of results.
Splicing support output files added as "tar" file to https://bitbucket.org/hotpollen/splicing-analysis as TabulateSplicingSupport/results/2022-09-08-results.tar.
Creating R code for organizing and sanity-checking results. Working on this fork and branch: https://bitbucket.org/aloraine/splicing-analysis/branch/IGBF-3172
Merged changes into master branch. Created new folder with consolidated results:
- TabulateSplicingSupport/results/ containing file 2022-09-08-results.txt
During our meeting I brought up using deep learning/machine learning to identify splicing events.
Here are some papers I found that were related to the idea:
code: https://majiq.biociphers.org/jha_et_al_2017/
code: https://github.com/Illumina/SpliceAI