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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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Genrich for single-end ATAC-seq data #24

Closed ShuangHe33 closed 4 years ago

ShuangHe33 commented 4 years ago

Thank you for the great tool Genrich. I have tried Genrich for paired-end ATAC-seq data and it worked very well to me.

I wonder whether the ATAC-seq mode is suitble for single-end ATAC-seq, since the cut sites only exsit in 5' end and I noticed that the '-y' option can analyze intervals centered on cut sites the 5' ends of unpaired alignments, so could the '-y' option work for the single-end data?

If not, is it compare for two biological data (one sequenced by 150bp pair-end and annother 51bp single-end) being called peak by two different tools (with different models)?

Thank you in advance !

jsh58 commented 4 years ago

I think this was addressed in #8, as well as the last section of #6. If not, please clarify.