Open caleblareau opened 7 years ago
Hi, We have run Hichipper on the HiC-pro outfiles and find that the number of Mapped_unique_quality reads reported is higher than Total_PETs. How is that possible? Are we missing something here. I am attaching one of the stat files as example. example.stat.txt
Thanks
The # of mapped unique quality interactions is derived from this:
cat "${WK_DIR}/${HICPRO_OUT}/hic_results/data/${SAMPLE}/"*Pairs | wc -l | awk '{print $1}'
What version of HiC-Pro are you using?
Thanks for your prompt response. We are using HiC-Pro 2.10.0
The problem was that hi-chipper is counting the valid pairs files twice. hic_results folder contains the following 2 files where file 2 is a subset of file 1:
sample1_trim_genome.bwt2pairs.validPairs
sample1_allValidPairs
So ideally it should be using only file2(sample1_allValidPairs) for counting, which is the deduplicated interaction file, isn't it?
I would like a to ask a couple of more questions as follows:
H3K27ac data the % is ~1%. Will this be considered a good or a bad quality chip efficiency or is it dependent on the antibody efficiency and other experimental factors?
Many thanks.
Munazah
On Fri, May 4, 2018 at 4:22 PM, Caleb Lareau notifications@github.com wrote:
The # of mapped unique quality interactions is derived from this:
cat "${WK_DIR}/${HICPRO_OUT}/hic_results/data/${SAMPLE}/"*Pairs | wc -l | awk '{print $1}'
What version of HiC-Pro are you using?
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Can get over 100% mapping from current bowtie2 parse