Question about Handling Genes in Repetitive Sequences and Blacklisted Regions

chsmiss / ATAC-amp

Searching for co-amplified regions on the genome from ATAC-seq data

MIT License

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Question about Handling Genes in Repetitive Sequences and Blacklisted Regions #4

Open liyapingdoct opened 1 month ago

liyapingdoct commented 1 month ago

Dear processors,

Thank you for developing this tool. I used it to generate results and found that some of the enriched genes are located in repetitive sequences. Should I simply ignore these genes, or is there a recommended way to modify the code to avoid interference from blacklisted regions and conserved chromatin open regions?

Any advice would be greatly appreciated!

Best regards, Li yaping Chongqing university

chsmiss commented 1 month ago

Sorry for such a late reply, you can use igv to see how this region compares to determine if it is retained or not after you get the candidate results, ecDNA amplified regions tend to see breakpoints on igv. Also, we are planning to upgrade atacamp to support filtering of blacklisted regions. I hope my reply is helpful for your use.