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Old 11-01-2012, 07:35 AM   #1
Location: Ireland

Join Date: Oct 2012
Posts: 42
Default Samtools flagstat - low % reads mapping


I'm working with RNA-Seq and using bowtie and tophat to align 65bp PE reads to a reference genome. My reads were sequenced from X.laevis and I'm attempting to first map to X.tropicalis (X.laevis genome is still draft version).

After trimming and filtering my reads I am left with 31*2 = 62M reads but running samtools on my accepted_hits.bam file shows that only 12M reads have mapped in total. I'm completely confused about why the number of reads mapping is so low - I've tried fine tuning the options in tophat (-r value, -N value) and using differently trimmed reads - but have seen little improvement on 20% mapping success.

In addition almost none of my reads pair properly (samtools flagstat 'properly paired' = 0.01%).

Any help would be hugely appreciated,

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