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

HLA_DRB1's coordinates(11000) exceed the generated fasta(10709) in the~/script/whole/annoHLA.pl script #48

Open
LeeDarian opened this issue Jan 10, 2025 · 2 comments
Open

HLA_DRB1's coordinates(11000) exceed the generated fasta(10709) in the~/script/whole/annoHLA.pl script #48

LeeDarian opened this issue Jan 10, 2025 · 2 comments

Comments

@LeeDarian
Copy link

WechatIMG9 WechatIMG8

The length of the generated fasta is 10709, but the script requires an index of 11000 and an error is encountered. How can I solve this problem? My sample is second-generation WGS data with a sequencing depth of 10X
@LeeDarian LeeDarian changed the title HLA_DRB1's coordinates(11000) exceed the generated fasta(10709) in the~/script/hole/nnoHLA.pl script HLA_DRB1's coordinates(11000) exceed the generated fasta(10709) in the~/script/whole/annoHLA.pl script Jan 10, 2025
@LeeDarian
Copy link
Author

Our reference genome is GCA_000001405.15_GRCH38_no-valtAnalysis_det.fna. Does it have any impact ？

@wshuai294
Copy link
Collaborator

Hi, I think this will not impact results of SpecHLA. samtool faidx will work even if the given interval is larger than the sequence length.

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
@LeeDarian @wshuai294