Hi! all,
I would like to calculate coverage from paired-end data. I can do this with bedtools but I want to make sure of one thing. That is to include full length insert in the coverage. For instance, I have 2 x 100 bp paired-end sequencing data and my average insert size is 500 bp. When I calculate the coverage I want to make sure that I include unsequenced part between two reads.
How can I make sure that coverage calculation includes unsequenced 300 nt part in a proper pair. Also, Is there a way of calculating coverage for both properly paired reads and singletons at the same time. Any tool is ok, Perl script, bedtools, samtools, bamtools etc.
Thank you for suggestions in advance.
I would like to calculate coverage from paired-end data. I can do this with bedtools but I want to make sure of one thing. That is to include full length insert in the coverage. For instance, I have 2 x 100 bp paired-end sequencing data and my average insert size is 500 bp. When I calculate the coverage I want to make sure that I include unsequenced part between two reads.
Code:
Read1 unsequenced part Read2 --------->|-------------------------------|<----------- 100 nt | 300 nt | 100 nt
Thank you for suggestions in advance.
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