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ATAC-seq peak calling?

I have some PE ATAC-seq data and i like to do peak calling using MACS2. I found that If I like use BAM file I have to use -f BAMPE option otherwise I have to change BAM file to BED and then use -f BED -- nomodel --shift -100 --extsize 200. Also, I found in ENDCODE https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit part 2a, that use bed file but there 2 files BEDPEand TAG file

-tagAlign file ${FINAL_TA_FILE}

-BEDPE file (with read pairs on each line) ${FINAL_BEDPE_FILE}

-Subsampled tagAlign file for CC analysis ${SUBSAMPLED_TA_FILE}

that I am not sure which one should be use as Input of MACS2. should I use TAG file as Input?

chip-seq macs2
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written by star star

Hello star!

Questions similar to yours can already be found at:

Please follow-up in the previous thread.

If you disagree with this please tell us why in a reply below. We'll be happy to talk about it.

Cheers!

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written by ATpoint ATpoint

Thank. But I like to know which file based on ENDCOD:

  • tagAlign file ${FINAL_TA_FILE}
  • BEDPE file (with read pairs on each line) ${FINAL_BEDPE_FILE}
  • Subsampled tagAlign file for CC analysis ${SUBSAMPLED_TA_FILE}

should be used as input of the MACS2.

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written by star star

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