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ay-lab / FitHiChIP

Statistically Significant loops from HiChIP data
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Reference genome used for inferring peaks from HiChIP data #92

Closed koushik20 closed 1 year ago

koushik20 commented 1 year ago

Hi,

This is more of a question than an issue. Firstly thanks for the detailed documentation. I am using "inferring peaks from HiChIP" data functions and want to know if the reference genome used in the -R option is of hg19 or hg38. Because I generated the .ValidPairs, .DEPairs, .REPairs, and .SCPairs using hg19.

Thank you!

ay-lab commented 1 year ago

Hi @koushik20 The -R option in your case should be "hg19". The parameter supports different reference genomes (hg19/hg38/mm9/mm10) depending on the valid pairs.

koushik20 commented 1 year ago

Hi @koushik20 The -R option in your case should be "hg19". The parameter supports different reference genomes (hg19/hg38/mm9/mm10) depending on the valid pairs.

Thanks for the response. But the -R parameter is only considering hs, mm, ce, dm as options. Shows an error when interpreting the "hg19" option.

ay-lab commented 1 year ago

Hi @koushik20 The "-R" parameter is same as the "-g" parameter in MACS2 (https://github.com/macs3-project/MACS/blob/master/docs/callpeak.md). If the reference genome is "hg19 / hg38", please use "hs". If the reference genome is "mm9/mm10", use "mm".