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Old 01-12-2011, 04:03 AM   #1
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 150
Post bowtie output

Hi,

I'm running bowtie with this command:
Quote:
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:
Quote:
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
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Old 01-12-2011, 04:34 AM   #2
andrehorta
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Location: Brazil - Belo Horizonte - UFMG

Join Date: Jan 2011
Posts: 14
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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...
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Old 01-12-2011, 12:45 PM   #3
csoong
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Location: Connecticut

Join Date: Jun 2009
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Seems like some PE-reads were mapped to more than 1 location but below your "m" threshold.
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