Hello all,
I am very new to bioinformatics so this might just be a stupid question....
I am using BWA and Samtools to map my sequence reads on a reference mitogenome, but the number of reads that can be mapped is very low - only about 100 reads. I suspect that BWA is only mapping the "complete" reads, so the reads that are 100bp (we did PE reads of 100bp on an Illumina HiSeq).
However, since we are working with highly degraded samples, we expect most of the fragments to be not longer than ~70bp. So if shorter reads are automatically kicked out, I am loosing >90% of my reads.
Does anyone know if it is the BWA script that kicks "shorter-than-expected" reads? Or how I can get to the shorter reads? Any help, suggestions, thoughts, comments, ect, are highly appreciated!
Cheers,
Johanna
I am very new to bioinformatics so this might just be a stupid question....
I am using BWA and Samtools to map my sequence reads on a reference mitogenome, but the number of reads that can be mapped is very low - only about 100 reads. I suspect that BWA is only mapping the "complete" reads, so the reads that are 100bp (we did PE reads of 100bp on an Illumina HiSeq).
However, since we are working with highly degraded samples, we expect most of the fragments to be not longer than ~70bp. So if shorter reads are automatically kicked out, I am loosing >90% of my reads.
Does anyone know if it is the BWA script that kicks "shorter-than-expected" reads? Or how I can get to the shorter reads? Any help, suggestions, thoughts, comments, ect, are highly appreciated!
Cheers,
Johanna
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