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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Merging replicates and downstream analysis with HOMER #357

Closed sanchari24 closed 3 years ago

sanchari24 commented 4 years ago

Hello, I have the paired end fastq files for two replicates. I want to merge them to increase the depth and run HOMER on the combined valid pairs.

Looking for suggestion for the best way to do this. Thank you.

nservant commented 4 years ago

Hi, If you put all fastq files in the same input folder, you will have one .validPairs file per fastq pair, and one .allValidPairs which is the merge of the two first. Otherwise, you can simply merge them by hand ! Best

sanchari24 commented 4 years ago

Hi thanks for the input, I could merge them. By the way, I wanted to ask if you have any idea about .AppleDouble files being created whenever I run HiC-Pro ?

./HiC_pro_result_V2/logs/CHiC_swnclf_mutant/.AppleDouble ./HiC_pro_result_V2/logs/CHiC_Col_control/.AppleDouble

nservant commented 4 years ago

Nope. Never heard about that :)