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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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the input file for diffhic #364

Closed QianzhaoJ closed 3 years ago

QianzhaoJ commented 4 years ago

Hi I tried to use diffhic for differential analysis of Hi-C data, and I found that the input files for diffhic need to be a name-sorted BAM file, so can I used the bam files provided by HiC-Pro directly ? By the way, I found that I need to assign and filtering fragments in diffhic, so maybe I can use the ValidPairs file in HiC-Pro as input files ? Thanks in advance ! Best wishes Qianzhao

nservant commented 4 years ago

Hi, If you run HiC-Pro with GET_PROCESS_SAM=1, it will generate a BAM file with all mapped reads and a flag 'CT' specifying if this a valid interaction (VI) or not. So you should be able to easily extract from the BAM file, the reads coming from valid interactions. Then, I'm not an expert of diffhic, but if there is a way to directly give valid interaction, then validPais should be ok. Best