Hi,
I'm working with RNA-Seq using 65 bp paired end reads. I'm having huge problems with mapping - after trimming and filtering reads (using fasts etc) only a small fraction (~20%) map to my reference genome (using bow tie/tophat). I'm attempting to map to a different species, which would explain this low number, but I also see that 0.01% of my PE reads pair 'properly' during alignment (using Samtools flagstat). I'm wondering if, during QC steps the reads have become unpaired, and thus fail to find mates during mapping.
Could anyone advise on this? Is there a way to filter PE reads together?
ANy help would be greatly appreciated,
N
I'm working with RNA-Seq using 65 bp paired end reads. I'm having huge problems with mapping - after trimming and filtering reads (using fasts etc) only a small fraction (~20%) map to my reference genome (using bow tie/tophat). I'm attempting to map to a different species, which would explain this low number, but I also see that 0.01% of my PE reads pair 'properly' during alignment (using Samtools flagstat). I'm wondering if, during QC steps the reads have become unpaired, and thus fail to find mates during mapping.
Could anyone advise on this? Is there a way to filter PE reads together?
ANy help would be greatly appreciated,
N
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