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.

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

No fasta corrected after run #22

Open
desmodus1984 opened this issue Sep 9, 2024 · 1 comment
Open

No fasta corrected after run #22

desmodus1984 opened this issue Sep 9, 2024 · 1 comment

Comments

@desmodus1984
Copy link

Hi,
I used CRAQ to correct my genome assembly using short-reads, and I expected to get the CRAQ-corrected FASTA fragments since I used -b T.
The code was as followed:
perl /home/juaguila/app/CRAQ/bin/craq -g myse-hapog.fasta -ngs MYSE.Q20.mapped.sort.bam -D craq-myse-corr -t 12 -b T

I mapped the reads to the assembly, then filtered out those with low mapping quality, then bam converted, sorted, and indexed the bam file.
I checked the craq-myse-corr folder and I didn't find any out_correct.fa file.

Short-reads aren't enough for correcting the query fasta?

Thanks;

@JiaoLaboratory
Copy link
Owner

Thanks for your use of CRAQ. Yes, short-reads are not be used to correct, which is usually false positive

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants