galaxyproject / galaxyproject/training-material

STARsolo 2.7.5b (Tutorial Feedback #989 Oct 29th 2020)

Open
#2,103 11 comments 0 reactions 0 assignees View on GitHub
transcriptomics
Dominant language
HTML
Stars
367
Forks
1.1k
Avg merge
16h 27m
Merged PRs (30d)
49

Description

looks like there are two independent issues here:
(ping @jennaj @mtekman @blankenberg )
- Yes, Homo_sapiens.GRCh37.75.gtf is not correctly auto detected as 'gtf' when uploaded from zenodo. I have seen this before (on other occasions), and it needs a fix in the sniffer (probably more than just a 'paper cut'?)
- STARsolo 2.7.5b (the current default on usegalaxy.eu) is broken (or need a different kind of transcripts annotation file?). The same inputs work with a previous tool version (e.g.: 2.7.2b1 )

Contributor guide

Open the contributing guide

Research direction

Reproduce both reported cases using the Zenodo upload of Homo_sapiens.GRCh37.75.gtf and the STARsolo 2.7.5b workflow on usegalaxy.eu. Start by examining the file-type sniffer and the tutorial's STARsolo inputs, then compare behavior with version 2.7.2b1. Done means the annotation is detected as GTF and the current workflow either runs with the documented inputs or clearly identifies the required annotation format.

Written by the indexing model from the issue text.

Assessment

Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.