Coverage statistics on single exons

gedoardo83 · 07-06-2011, 05:40 AM

Hi,

I'm engaged in an exome sequencing project.
I have done my NGS exome sequencing using illumina platform with an average 50X coverage and the Agilent SureSelect capture kit.
I've aligned all the reads and generated the corresponding bam file. Now I'm doing same data analysis but visually inspecting the aligned reads, I've noted that some exons (from RefSeq) seem to have no coverage at all.
So I'm interested in a report on exact coverage for the various exons. In particular is there a way to know if there are exons with no coverage, how many of them and eventually which ones?

Thanks,
Edoardo

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07-06-2011, 05:40 AM	#1
gedoardo83 Junior Member Location: Brescia, Italia Join Date: Jun 2011 Posts: 2	Coverage statistics on single exons Hi, I'm engaged in an exome sequencing project. I have done my NGS exome sequencing using illumina platform with an average 50X coverage and the Agilent SureSelect capture kit. I've aligned all the reads and generated the corresponding bam file. Now I'm doing same data analysis but visually inspecting the aligned reads, I've noted that some exons (from RefSeq) seem to have no coverage at all. So I'm interested in a report on exact coverage for the various exons. In particular is there a way to know if there are exons with no coverage, how many of them and eventually which ones? Thanks, Edoardo