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Old 07-13-2016, 03:36 AM   #1
moistplus
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Location: Germany

Join Date: Feb 2016
Posts: 40
Default Discordant result between bowtie2 and sam filtering

Hello,

I have a list of contaminants that I want to filter out from my paired end:

Code:
bowtie2 -x contaminants -1 pair1.fastq -2 pair2.fastq -S out.sam
Now I want to extract only unmapped reads from the .sam file but I want to keep only paired end.

So if read1 map somewhere and read2 not, I want to discard these PE.

Code:
samtools view -f 4 -bu input.bam | samtools view -f 8 -bu - | java -jar  picard-tools/picard.jar  SamToFastq  I=/dev/stdin F=out1.fq.gz F2=out2.fq.gz  FU=unpaired.fq.gz

I got a problem, the output of bowtie 2 is :

Quote:
5317475 reads; of these:
15317475 (100.00%) were paired; of these:
15155323 (98.94%) aligned concordantly 0 times
155208 (1.01%) aligned concordantly exactly 1 time
6944 (0.05%) aligned concordantly >1 times
----
15155323 pairs aligned concordantly 0 times; of these:
95593 (0.63%) aligned discordantly 1 time
----
15059730 pairs aligned 0 times concordantly or discordantly; of these:
30119460 mates make up the pairs; of these:
29853788 (99.12%) aligned 0 times
195884 (0.65%) aligned exactly 1 time
69788 (0.23%) aligned >1 times
2.55% overall alignment rate
which mean I should have 15155323 PE right ?

But when I do :

Code:
grep '@' out1.fastq | wc -l
I got : 14798490 PE

1) What's wrong with my command ?
2) Moreover my unpaired.fq.gz is empty
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Old 07-13-2016, 09:30 AM   #2
lindenb
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Location: France

Join Date: Apr 2010
Posts: 143
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cross posted https://www.biostars.org/p/201555/
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