Entering edit mode
8.5 years ago
Mikee
•
0
Hi :)
I am in search of an easy method to list all sequencing gaps for MiSeq-NexteraXT-Workflow.
The result should be a list of all target-regions (exons+20bp-padding) which at some point fall below a CoverageDepth of 50x. So we can reanalyze those exons via Sangerseq.
For Illumina-Enrichment Workflow this was easily done via the "gaps.csv"-File by modifying the samplesheet with "MinimumCoverageDepth,50". Sadly "gaps.csv" are not given in the NexteraXT-method :(
I am the typical Windows-User and was happy until now with Excel, VariantStudio and IGV-Browser :D Is there a way to get such a gaps-list without Linux-Command-Line-Tools like BedTools or is there no way around?
Thx a lot!
