Inflated alignment stats about hichipper

[smza]

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

[caleblareau]

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?

[smza]

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: 1. sample1_trim_genome.bwt2pairs.validPairs 2. 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: 1. we would to like to know what should be the threshold for “% of fraction of total reads that are in loops" to be considered a good quality ChIP. We have seen in your 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? 2. How do you evaluate the biological and/or technical replicate consistency? Do you have any QC metrics for doing so? Many thanks. Munazah

…

On Fri, May 4, 2018 at 4:22 PM, Caleb Lareau ***@***.***> 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? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#15 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ATSwicog0OlkwL-RmBfxMN-uegMYObhmks5tvHIwgaJpZM4Nhm65> .