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Old 03-06-2013, 11:48 AM   #1
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Default Bowtie: unaligned reads when mapping "max" reads


I am mapping 2x100 Illumina reads against hg19 using Bowtie using a tiered approach. I want separate output files for reads that map to 1 location and reads that map to 2 locations.

In Tier 1, I set m=1 and use --max to save the reads that mapped to more than 1 location. (eg: m 1 --max max.fastq)

In Tier 2, I set m=2 and map the reads from the max.fastq file. Usually, the number of unaligned reads in this step is 0 (as would be expected). Sometimes however there are unaligned reads. Does anyone know why that is?

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