Hi,
I've numerous sequences which are not found in the reference genome of my species. I would like to determine the number of copy of these ORFs in each of my individual along with the reference ORFs based on coverage analysis. Most of the software I've found use whole genome analysis and don't seem well adapted for small (around 1kb) unique ORFs. Do you have any advice or software which could work well with this kind of data?
Thanks!
2 answers
One solution could be to use a sliding window approach to compare coverage between samples. The window coordinates could be generated with BedTools and the reads quantified using Featurecounts. Something similar has been discussed previously as well as this review article .
I would add split-read/paired-end callers for increased sensitivity and breakpoint resolution (e.g Delly, Lumpy.,.). Here you can find a list of available software for SV detection
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