Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Incorrect columns in Salmon transcript files #775

Closed
artemyzhigulev opened this issue Mar 1, 2022 · 1 comment
Closed

Incorrect columns in Salmon transcript files #775

artemyzhigulev opened this issue Mar 1, 2022 · 1 comment
Labels
bug Something isn't working
Milestone
3.7

Comments

@artemyzhigulev
Copy link

Description of the bug

Hi, I check the salmon.merged.transcript_tpm.tsv file now. For some reason first two columns are duplicated tx names, which results in a mess with column names.

Command used and terminal output

tx	gene_id	sample1
ENST00000456328	ENST00000456328	ENSG00000223972
ENST00000450305	ENST00000450305	ENSG00000223972
ENST00000488147	ENST00000488147	ENSG00000227232
ENST00000619216	ENST00000619216	ENSG00000278267
ENST00000473358	ENST00000473358	ENSG00000243485
ENST00000469289	ENST00000469289	ENSG00000243485
ENST00000607096	ENST00000607096	ENSG00000284332
ENST00000417324	ENST00000417324	ENSG00000237613
ENST00000461467	ENST00000461467	ENSG00000237613

Relevant files

No response

System information

No response
@artemyzhigulev artemyzhigulev added the bug Something isn't working label Mar 1, 2022
@drpatelh drpatelh added this to the 3.7 milestone Apr 26, 2022
@drpatelh drpatelh changed the title Problem with transcript files Incorrect columns in Salmon transcript files Apr 29, 2022
drpatelh added a commit to drpatelh/nf-core-rnaseq that referenced this issue Apr 29, 2022
@drpatelh
Fix nf-core#775
a8ede59
@drpatelh drpatelh mentioned this issue Apr 29, 2022
Merged
@drpatelh
Copy link
Member

Fixed in #815

drpatelh added a commit that referenced this issue Apr 29, 2022
@drpatelh
Merge pull request #815 from drpatelh/updates
c5bff79 
Fix #762 and #775
@drpatelh drpatelh mentioned this issue May 2, 2022
Closed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
bug Something isn't working
Projects
None yet
Milestone
3.7
Development

No branches or pull requests
2 participants
@drpatelh @artemyzhigulev