Hi NGS user,
I'm developing a script to remove PCR duplicates. I observed that samtools rmdup function doesn't always work well.
I'm using bioperl object and Bio:B::Sam utilities.
I have to distinguish if a bam is paired-end or single-read. Is there anyway to do this by Bio:B::Sam?
To remove duplicate,
if the NGS experiment is a single read, I considered duplicates read with the same start/end and with the same sequence.
If the NGS experiment is a paired end, a read is a PCR duplicates if has the same start of the first mate and the end of the second mate. Is it right?
Thanx a lot!
ME
I'm developing a script to remove PCR duplicates. I observed that samtools rmdup function doesn't always work well.
I'm using bioperl object and Bio:B::Sam utilities.
I have to distinguish if a bam is paired-end or single-read. Is there anyway to do this by Bio:B::Sam?
To remove duplicate,
if the NGS experiment is a single read, I considered duplicates read with the same start/end and with the same sequence.
If the NGS experiment is a paired end, a read is a PCR duplicates if has the same start of the first mate and the end of the second mate. Is it right?
Thanx a lot!
ME
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