Update GTF names in TOPMed_RNAseq_pipeline.md #114
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Fix GTF names so that the files created by collapsing annotation, adding ERCC match those used as input for subsequent steps. And that the right GTF (including ERCC, with or without collapsing as appropriate, v39 not v30) is referred to in subsequent steps.
Currently, the script acts as if STAR was run with outputting a sorted BAM, even though output is unsorted BAM. I added a sorting step, and changed some of the variable names accordingly.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fix GTF names so that the files created by collapsing annotation, adding ERCC match those used as input for subsequent steps. And that the right GTF (including ERCC, with or without collapsing as appropriate, v39 not v30) is referred to in subsequent steps.