HMMRATAC
HMMRATAC copied to clipboard
LiuLabUB
HMMRATAC peak caller for ATAC-seq data
This issue ticket is to track our progress to build a CI/CD pipeline for HMMRATAC in TravisCI. We need to implement: 1. Auto-compilation and packaging triggered by each commit 2....
samtools view -H ATACseq.sorted.bam| perl -ne 'if(/^@SQ.*?SN:(\w+)\s+LN:(\d+)/){print $1,"\t",$2,"\n"}' > genome.info results in an empty genome.info file I am using UBUNTU 20.04.5 Does anyone have any suggestion?
Hi, thanks for the tool! I am currently comparing a few tools to establish a multi-omic single-cell RNAseq and single-cell ATACseq pipeline. I am trying HMMRATAC and saw in the...
**Use case** A clear and concise description of what the use case is. For example: my data is from [...] **Describe the problem** A clear and concise description of what...
Why the 4th column of bedgraph file values are E0, E1 and E2? What is the meaning of these values?
Hello: I thought the 4th column of `bedgraph` file should be a digital number which is the value of the region. But for the `HMMRATAC` output, why the 4th column...
This is a screenshot of my gappedPeak file in IGV.  I'm guessing the blue bar is my open chromatin region while the extended line is my nucleosome? I understand...
Hi @EvanTarbell and @taoliu Question: Does one need to MARK duplicates so that HMMRATAC can remove duplicates OR does HMMRATAC remove them. Please advise. https://github.com/LiuLabUB/HMMRATAC/blob/master/HMMRATAC_Guide.md (last edit 19-Aug-2019) ``` It...
Hello, I run ``` samtools view -H C1.FINAL.BAM | perl -ne 'if(/^@SQ.*?SN:(\w+)\s+LN:(\d+)/){print $1,"\t",$2,"\n"}' > genomeinfo/C1.FINAL.BAM java -jar ~/HMMRATAC_V1.2.10_exe.jar -b C1.FINAL.BAM -i C1.FINAL.BAM.bai -g genomeinfo/C1.FINAL.BAM ``` But got this error: ```...