Yichao Li

Why create different resolutions for different fragment size "Binning"?

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Fragment bin group | Resolution -- | -- 36-149 | 1 150-224 and 225-324 | 2 325-400 | 5 I didn't get the point. It feels that this method tends...

Hi, I found it's OK to run `delly call -g /home/yli11/Data/Human/hg38/fasta/hg38.fa -v merged_germline.bcf -o OUTPUT -x /home/yli11/Data/Human/hg38/annotations/human.hg38.excl.tsv INPUT.bam` But once I added `-d sv_support.gz` to the above command. It had...

Find Broken Motifs for a combination of SNPs

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Hi, Suppose that you have two SNPs that are adjacent, currently, motifBreakR will analyze these two SNPs separately, however, I'm looking for a motif that could be broken by the...

how to reduce the number of clusters?

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Currently, the result has 100+ clusters. How to reduce this number? Thanks, Yichao

 Hello, Please see the illustration. The expected mutation from PrimeDesign Input is G4CTTCT. When mapping the PBS and RTT sequences, the mutation I got is actually the deletion of...

epic2-bw KeyError: 'mapq'

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When running with bam files (-t 1.bam -c 2.bam). I got the following error. Traceback (most recent call last): File "/home/yli11/.conda/envs/diffPeaks/bin/epic2-bw", line 174, in main(args) File "/home/yli11/.conda/envs/diffPeaks/lib/python3.7/site-packages/epic2/bigwig.py", line 97, in...

need examples, epic2, epic2-bw, epic2-df

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I think epic2 is for regular peak calling (e.g., TF-chip vs. input)? epic2-df is for differential peak calling (treatment vs. control)? Then what is epic2-bw for? Thanks, Yichao

use epic2 for ATAC-seq?

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Since epic2 is optimized for diffuse peaks (correct me if it is not), is it OK to run epic2 for narrow peaks, like regular TF ChIP-seq? I'm trying to find...

Hello, Thank you for the great tool. One question I have after reading the paper, also looking the code, is seems that the peak-gene pairs are predicted using cells from...