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

genrep4humans: fasta from transcriptome #5

Open
delafont opened this issue Nov 5, 2013 · 2 comments
Open

genrep4humans: fasta from transcriptome #5

delafont opened this issue Nov 5, 2013 · 2 comments

Comments

@delafont
Copy link
Contributor

delafont commented Nov 5, 2013

genrep4humans.py -a mm10 -i 2 -t chr17:69967073-70821413

will return a single sequence, but it would be much more useful to have the sequence from each transcript in the specified region separately (for instance, when there is an SNP and one wants to know if it is synonymous).
@fabdavid
Copy link
Member

fabdavid commented Nov 5, 2013

the option -i currently works to retrieve full transcriptome and not to retrieve a sequence region.

@jrougemo
Copy link
Member

jrougemo commented Nov 5, 2013

As far as I understand -i has no effect here (this is the genomic sequence that you get).
By the way chr17:69967073-70821413 has no meaning as a reference on the transcriptome / exonome

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@fabdavid @jrougemo @delafont