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Old 08-18-2016, 12:38 AM   #1
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Location: The Netherlands

Join Date: Apr 2008
Posts: 6
Default Bowtie2 paired end --un-conc

Hi all,
As part of a normalization strategy for a ChIP-seq experiment, I am using Bowtie2 to align paired end ChiP-seq reads first to the fly genome and then take the unaligned reads and align to the human genome.

In order to output the reads that fail to align to fly concordantly I'm using --un-conc like this:

bowtie2 -p 8 --no-unal --un-conc unaligned.fq -x DMBDGP6.dna.primary_assembly -1 sample1_R1.fastq.gz -2 sample2_R2.fastq.gz -S output.sam

This produces two fastq files called unaligned.1.fq and unaligned.2.fq (.1 and .2 added to make per-mate filenames). I want to use these files downstream to align to the human as paired-end data. But, the output is different in length (different numbers of reads), which causes Bowtie2 to fail when mapping paired-end with -1 and -2.

Is there a way to have Bowtie2 output only the paired reads to these two files that fail to align concordantly? Or do I need to align downstream as independent unpaired reads, which completely defeats the purpose of using PE reads in the first place.

Thanks for the advice!
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