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Old 01-09-2018, 12:20 AM   #3
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Location: Singapore

Join Date: May 2016
Posts: 6

Iím sorry, I didnít explain the issue properly. Iím working on CG WGS data with avg read depth of 40x. The QC metrics looks good for all parameters and the alignment rate is 97.43%. However, I had used cgaTools to convert tsv files provided by CG to BAM. When I visualize these BAM files on IGV, I see minimal coverage at all exons and major parts of introns for all genes (See example image attached). The trend is normally scant coverage hills at junction of intron and exon. I believe something went wrong in my conversion step. Can anyone please suggest a solution for this?
Or is there any other visualization tool specific for CG data that I should be using?Ē

The IGV snapshots is attached herewith.

Thanks in advance
Attached Files
File Type: ppt IGV_IMAGE.ppt (243.0 KB, 5 views)

Last edited by raman91; 01-09-2018 at 12:48 AM.
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