Some Question About Hi-C data Analysis

Question

[Ashley]

Recently, I am learning HiC data analysis using Juicer. I have two types of samples. And each of them has 3 replicate. How can I merge them? Just merge .bam files and filter duplicates from PCR?

[Ashley]

My script is that

juicer.sh -d /$path/merge -s "MboI" -S final -p /$path/hg19.chrom.sizes -y /$path/hg19_MboI.txt -z /$path/bwaindex/hg19.fa -D /$path/juicer -t 5

Error: no fastq/ folder

[Ashley]

I mapped the fastq files using bwa. I don't want to map them again.

[ATpoint]

Please use ADD COMMENTfor commenting on your toplevel question or directly edit the question itself. Also, please use the code button 101010 to indicate code.

[Ashley]

Thanks a lot! Give my best wishes!