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

Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2 #138

Open
rason81 opened this issue Sep 4, 2023 · 1 comment
Open

Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2 #138

rason81 opened this issue Sep 4, 2023 · 1 comment

Comments

@rason81
Copy link

rason81 commented Sep 4, 2023 •
edited
Loading

bowtie1 with versions greater than 1.2.0 are not compatible with Tophat (v2.1.1), reporting things like "./SeqAn-1.4.2/seqan/basic/basic_exception.h:236 FAILED! (Uncaught exception of type St11logic_error: basic_string::_S_construct NULL not valid)".
Possibly this issue is related to generation of *_genome.bwt.samheader.sam, because recent bowtie versions cannot generate sam headers with the empty input.
Although there is alternative for Tophat, it is still at some point the optimal one.
So, how to fix this issue?
@rason81 rason81 changed the title Comparability of Bowtie1 (v1.2.0 or later) with Tophat2 Compatibility of Bowtie1 (v1.2.0 or later) with Tophat2 Sep 4, 2023
@yuanlizhanshi
Copy link

i encountered the same problem, how did you slove this?

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
2 participants
@rason81 @yuanlizhanshi