I have a paired end Illumina exome data set that might have overlapped at the ends. My fragment size has 105 bp. I aligned my samples with bwa and generated my bam files with samtools.
My question is:
Is there any way to determine how many reads overlapped?
How can I determine the distance between the paired ends (in case they didn´t overlap) or how much they overlapped?
If this percentage is high, I am thinking about reanalyzing my data generating fragments of 75 or 50bp. Do you think that’s correct? Which percentage could be the cut-off to consider it high?
Thanks
My question is:
Is there any way to determine how many reads overlapped?
How can I determine the distance between the paired ends (in case they didn´t overlap) or how much they overlapped?
If this percentage is high, I am thinking about reanalyzing my data generating fragments of 75 or 50bp. Do you think that’s correct? Which percentage could be the cut-off to consider it high?
Thanks
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