Hi everyone,
I had sequenced ancient museum samples on Illumina Hiseq 4000 platform. After running through typical pre-processing steps to generate a bam file (eg. cutadapt, bwa mem, mark duplicate, indel realignment). I then input the bam files into qualimap and obtained very strange coverage histograms (50x) (attached). I obtained coverage histograms with a similar pattern even after rescaling the bam file using mapdamage 2.0.
I am wondering what is the reason for this pattern in coverage?
Thanks in advance!
I had sequenced ancient museum samples on Illumina Hiseq 4000 platform. After running through typical pre-processing steps to generate a bam file (eg. cutadapt, bwa mem, mark duplicate, indel realignment). I then input the bam files into qualimap and obtained very strange coverage histograms (50x) (attached). I obtained coverage histograms with a similar pattern even after rescaling the bam file using mapdamage 2.0.
I am wondering what is the reason for this pattern in coverage?
Thanks in advance!
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