Hi,
A bowtie question of output interpretation,
CMD:
bowtie -p 16 -a --best --strata -q -S --sam-nohead -q -v 2 target single_dir/single_fa > single_dir/single_fa.pre.sam
STDERR:
# reads processed: 32354340
# reads with at least one reported alignment: 15905262 (49.16%)
# reads that failed to align: 16449078 (50.84%)
Reported 24030582 alignments to 1 output stream(s)
I could only locate a few examples online of bowtie stderr, and in the singular stderr example in the bowtie manual the #reads reported = # alignments.
Is it that in the event of a tie (two alignments equally as "good") that both are reported?
What I would like is for all alignments to be considered ("-a"), yet only those reported that are best for each read (presumably "--best --strata"). I've tried adding "-k 1" to the command above, but the output is identical.
Any suggestions/interpretations?
A bowtie question of output interpretation,
CMD:
bowtie -p 16 -a --best --strata -q -S --sam-nohead -q -v 2 target single_dir/single_fa > single_dir/single_fa.pre.sam
STDERR:
# reads processed: 32354340
# reads with at least one reported alignment: 15905262 (49.16%)
# reads that failed to align: 16449078 (50.84%)
Reported 24030582 alignments to 1 output stream(s)
I could only locate a few examples online of bowtie stderr, and in the singular stderr example in the bowtie manual the #reads reported = # alignments.
Is it that in the event of a tie (two alignments equally as "good") that both are reported?
What I would like is for all alignments to be considered ("-a"), yet only those reported that are best for each read (presumably "--best --strata"). I've tried adding "-k 1" to the command above, but the output is identical.
Any suggestions/interpretations?