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

The -m option only results in some "many mapped" reads being supressed #94

Open
Riptides opened this issue Jul 11, 2019 · 0 comments
Open
Assignees

Comments

@Riptides
Copy link

Riptides commented Jul 11, 2019

bowtie \
	-v 0 \
	-a \
	-m 20 \
	--threads ${THREADS} \
	--max ${MANY} \
	-f \
	--un ${UNMAPPED} \
	${REF} \
	${FASTA} \
	> ${OUTFILE}

From my understanding, the above command should output all reads that align perfectly more than 20 times to ${MANY} and output all perfect alignments for reads that align 20 or fewer times to ${OUTFILE}. I am finding multiple instances, however, where a read will have over 20 perfect alignments reported in ${OUTFILE} and not be listed in ${MANY}.

Is this a bug or is my understanding of the flags incorrect?

Tested with both 1.2.2 and 1.2.3

@ch4rr0 ch4rr0 self-assigned this Jul 11, 2019
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