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Posts by e.jacobson
... I ended up getting advice from someone who uses HiCUP and diffHiC together frequently, and they suggested this: 1) .bam files have to be name sorted: samtools sort -n myData.bam > myData.sorted.bam (check if reads have /1 and /2 at the end; this will cause problems) 2) HiCUP digest fil ...
... I have mapped and filtered my Hi-C reads using HiCUP (https://www.bioinformatics.babraham.ac.uk/projects/hicup/) and it is too computationally intensive to align the reads again with diffHiC (each library is ~400 million 150bp pairs). I was wondering if someone could recommend the best way to get th ...
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