bowtie output

[frymor]

Hi,

I'm running bowtie with this command:

bowtie -a --best --strata -m 10 -n 2 -l 22 -q --un mut.unmapped -t -p 2 -5 11 --chunkmbs 256 --max mut.maxHits -S d_melanogaster_fb5_32 -1 s2_1_sequence.fq -2 s2_2_sequence.fq output.sam

this what I am getting on my output when I am running bowtie:

Time loading reference: 00:00:01
Time loading forward index: 00:00:01
Time loading mirror index: 00:00:01
Seeded quality full-index search: 05:03:50
# reads processed: 42867915
# reads with at least one reported alignment: 21891058 (51.07%)
# reads that failed to align: 20748783 (48.40%)
# reads with alignments suppressed due to -m: 228074 (0.53%)
Reported 23418877 paired-end alignments to 1 output stream(s)
Time searching: 05:03:53
Overall time: 05:03:53

For each of the paired-end fastq files I have 42867915 reads. this is also the sum of the three #-lines.
What is the meaning of the number in the last line? -23418877

Thanks
Assa

[andrehorta]

I don't know too.

Process C:/ufmg/brca_diagnostic/FASTQ/SRR062634.filt.fastq
# reads processed: 308846
# reads with at least one reported alignment: 833 (0.27%)
# reads that failed to align: 308013 (99.73%)
Reported 833 alignments to 1 output stream(s)
# reads processed: 308846
# reads with at least one reported alignment: 794 (0.26%)
# reads that failed to align: 308052 (99.74%)
Reported 794 alignments to 1 output stream(s)
Look for mutations...

[csoong]

Seems like some PE-reads were mapped to more than 1 location but below your "m" threshold.