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wbaopaul / scATAC-pro

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
MIT License
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Question: why MACS2 is forced to run SE mapping? #50

Closed Puriney closed 2 years ago

Puriney commented 2 years ago

https://github.com/wbaopaul/scATAC-pro/blob/b6380d961bd0aae9da1ff0acea7f95e8138c43f1/scripts/call_peak.sh#L28

Hello, I have 3 questions.

  1. How can I let MACS2 to run in the PE mode because my input sequencing reads are pair-end?

I thought the parameter in the config file can set this process. But I did not see it used here. 

isSingleEnd = FALSE

  1. Is there any particular reason scATAC-pro force MACS2 to run in single-end mode?

  2. How the above isSingleEnd parameter affect the entire process? Where is it used?

Many thank.

wbaopaul commented 2 years ago

Thanks.This is a bug. I just pushed a fix for this issue to branch v1.4.1, it will automatically use BAMPE if isSingleEnd=FALSE and BAM otherwise. Pleas use branch v1.4.1. (I will merge the updates to master branch soon). isSingleEnd is mostly used in the dex_fastq and trimming module.