I am working on project where I need to get ALL hits to each read - defined fairly stringently. I tried to use bowtie2 with a command like this:
bowtie2 --threads 20 --reorder --score-min L,-0.5,-0.2 -a -x trdb -U R15.fq -S 15_tr.sam
My reads are 100 bp long hence the parameters for match are fairly stringent here. I expected that bowtie2 might take a while but will complete the job. Without the '-a' flag the job completed in about 30 mins. But with -a, I was waiting nearly 3 days and still undone.
To judge from the sam file, bowtie2 completed the alignments for about 70K of the reads reads (in ~ 10 mins) and then kept spinning with no writes to the sam file thereafter.
I know bowtie2 manual says it is not optimized for the -a flag. But this looks much worse than unoptimized. Its unusable. Anyone have experience with this?
Thanks,
Gulu
bowtie2 --threads 20 --reorder --score-min L,-0.5,-0.2 -a -x trdb -U R15.fq -S 15_tr.sam
My reads are 100 bp long hence the parameters for match are fairly stringent here. I expected that bowtie2 might take a while but will complete the job. Without the '-a' flag the job completed in about 30 mins. But with -a, I was waiting nearly 3 days and still undone.
To judge from the sam file, bowtie2 completed the alignments for about 70K of the reads reads (in ~ 10 mins) and then kept spinning with no writes to the sam file thereafter.
I know bowtie2 manual says it is not optimized for the -a flag. But this looks much worse than unoptimized. Its unusable. Anyone have experience with this?
Thanks,
Gulu
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