chipseq_pipeline

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Bumps [numpy](https://github.com/numpy/numpy) from 1.11.3 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...

dependabot[bot]

JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa"

1

Got an error at the JSD step. I used nth=1 (I tried with more but they somehow did not work either, or said "not enough resources"), and on a server...

liliaevgeniou

Can't download hg19 genome data

2

Hello, There is an issue downloading hg19 genome data. Stuck at "HTTP request sent, awaiting response..." hg38 can be downloaded. Can you please solve? Thanks!

tfchipchip

job submission command

2

Hi Jin, I have 2 tested files ran successfully, the command I used is as below. N2 results look weird as shown in washU browser. I guess my command is...

LiangMa2017

Trimmed data-sets

1

Hello, Is it correct to run the pipeline after trimming adaptors in paired-end data-sets? I get different read lengths. Raquel

pixelRaquel

Hi, I have ChIP-seq data for one patient and one normal person as well as input for both of them (they run at different batch and each batch has a...

yingsun-ucsd

hi, I run phantompeakqual on my duplicates removed bam files and got an error shown in the title. later, I re-run the same command but on bam files before `samtools...

crazyhottommy

Update bgd to bw conversion in callpeak_macs2.bds

2

The bedgraph to BigWig conversion step throws an error on my system for all my files: `(...)pooled.tagAlign.fc.signal.srt.bedgraph is not case-sensitive sorted at line 1879. Please use "sort -k1,1 -k2,2n" with...

florianduclot