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?
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
I mapped the fastq files using bwa. I don't want to map them again.
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Thanks a lot!
Give my best wishes!
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