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jsh58 / Genrich

Detecting sites of genomic enrichment
MIT License
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single end data ATAC-seq mode #8

Closed ShuangHe33 closed 5 years ago

ShuangHe33 commented 5 years ago

Hi,thank you for the great software. According to your manual, I'm wondering that is it appropriate to apply -j -y mode to single-end ATAC-seq data(51 bp) since only one cut site of a read can be provided ? Now I have two replicates , one is paired-end and the other one is single-end , I'm worried that it will find more peaks in the paied-end ATAC-seq data than the single-end data use -j -y mode. Could you please give me some advice? Thank you in advance.

jsh58 commented 5 years ago

First of all, with single-end reads, you must specify -y for any intervals to be interpreted. Yes, only one interval will interpreted with single-end reads; half as many as with paired-end reads, but the background will also be half as much. So there won't necessarily be more peaks with paired-end reads. The best suggestion is try it out and see what happens.

ShuangHe33 commented 5 years ago

Hi, I applied Genrich to one of my single-end ATAC-seq data with '-y -j -d 100 ' and it detected 28757 peaks while the number of peak was 37675 performed by MACS1.4 (default parameters). Usually Genrich can find more peaks of paired-end ATAC-seq data (with parameters '-y -j -d 100') compared to MACS1.4 (default parameters) according to my experience. Hope this information is helpful.