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Old 01-14-2020, 06:52 AM   #4
r.rosati
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Location: Brazil

Join Date: Aug 2015
Posts: 92
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Hi! Which platform was used to generate the WES data? If it's an Ion Torrent, some time ago I made this small script for this exact purpose. It can be used with Galaxy if you like.
If it's Ion Torrent data and you want to try it, you'd only need to provide gene names, the BAM file, the Ampliseq targets bedfile, and an annotated source (instructions are in the readme). It will return info on regions fo your genes of interest that are plainly not covered by the panel, and regions with low coverage, strand bias, and low coverage on one strand (the base parameters that can affect basecalling). It also informs you if the poorly covered region is actually within the CDS or splicing regions, or not. And it gives you an easy copy-and-paste text to check the data on IGV.
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