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WGLab / LinkedSV

MIT License
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inquiries on blacklist region #30

Open distilledchild opened 2 years ago

distilledchild commented 2 years ago

Fristly, I am really thankful for the interesting tool, and I am very excited to try it now. In the middle of preparing the process, I found that a blacklist region file is not available for my genome, (rat, rn7). Could you explain how to generate it please? Now I am running the tool with a blacklist region file from liftover mm10 blacklist region, but I want to try generating it myself. Also, I found that there is 2D blacklist region file which I can use too. It sounds like it has the list of regions where barcodes are overlapping. Could you give me some tips to make it too? If I have two blacklist region files, how could I use when executing the command?

Thank you !

fangli80 commented 2 years ago

The blacklist region and the 2D blacklist region for human were generated from 12 healthy human genomes. These regions have unusual high coverage or barcode overlapping but no SVs.

If you have sequencing data of some wild-type rats, I can help generate this. If only have one sample, you can use a blank file as the blacklist file, but this may generate some false-positive calls. In this case, manual validation by IGV or experimental validation is needed to confirm the SV calls.

Thanks, Li

distilledchild commented 2 years ago

@fangli80 Thank you for the reply! I have multiple samples. (I am dealing with recombinant rat strains.) So, Which data would be needed to generate the files?

fangli80 commented 2 years ago

Hello @theshowmustgolangon , bam files are need to generate these files.