I am new to HiC and using HiCUP to analyse HiC data (I will try other pipelines and combination of software eventually).
/tools/hicup --zip --bowtie2 /tools/bowtie2-184.108.40.206-linux-x86_64/bowtie2 --index /hg38/hg38 --digest /hg38/Digest_hg38_HindIII_None_15-12-15_27-10-2021.txt R1.fastq R2.fastq
For now, I aligned the read file and HiCUP outputs a pair BAM file (read 1 and read are paired after R1 and R2 independent alignment).
I want to use the output of HiCUP (SAM format) to prepare input for HOMER (makeTagdirectory). The input should be two read files aligned separately (eg R1.sam and R2.sam). But since HiCUP gave me only one paired BAM, I was wondering how to prepare such input.
I read here that says
BAM file produced by HiCUP is used to create a tag directory using Homer for further analysis that includes interaction matrix generation, compartments and identifying significant interactions.
But HOMER (makeTagdirectory) require two sam R1 and R2 separately.
Two things I could think of here is either:
Prevent pairing after alignment by HiCUP (but this option is not available).
Split paired BAM to R1.sam and R2.sam (I don't know if it is the right way to do).
If anyone has prior experience or suggestion, I would appreciate the help.