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Hi Tan,
Happy Monday!
I remember reading in the readme of this repo that hickit is much faster than dip-c. I know that hickit does not implement the 3D imputation step like Dip-c does. But during…
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Dear developers,
Firstly, I would like to express my appreciation for the detailed ATAC-seq pipeline that you developed. As a PhD student, I find this tool extremely helpful in analyzing ATAC-seq d…
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Hi,
I want to used your software to do a QC on my ATACseq data performed on cucumis melo species. I'm wondering if it's possible and how I can integrate my genome on your image ?
Thanks in adv…
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Hi,
Thanks very much for developing this fantastic resource. I am currently studying comparing the HiCexplore insulation scores between TAD types and just wanted to clarify some interpretation. In…
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Hi,
I want to know what file to use in the below two steps;
TOBIAS ATACorrect --bam test_data/Bcell.bam --genome test_data/genome.fa.gz --peaks test_data/merged_peaks.bed --blacklist test_data/…
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Hi Natsuhiko,
Could you explain how reference allele bias can be calculated per SNP? I understand how reference allele bias can be calculated genome-wide per individual by taking the average refere…
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There seems to be some interest in having support for DPD. Most likely we would want to use the method described in http://arxiv.org/abs/cond-mat/0602523. It would involve writing a new Integrator t…
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Thank you for your great work!
I would like to ask if the genomic region of the bam file needs to be exactly the same as the range of peak.bed? my peak.bed is just a partial chromatin open region of …
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