atacseq
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nf-core
ATAC-seq peak-calling and QC analysis pipeline
Every run I receive the below warning: `WARN: Output channel ch_gene_bed overrides another variable with the same name declared in the script context -- Rename it to avoid possible conflicts`...
Hello, I've just noticed that IGV doesn't like dots in relative paths in `igv_session.xml` 🧐 The session is normally loaded, but saving throws the "popular" Java NullPointerException. So here is...
`read.delim` is used [here](https://github.com/nf-core/atacseq/blob/1b3a832db5a53c92c2c89a4d6d79455e860461ad/bin/featurecounts_deseq2.r#L62). That function implicitly replaces hyphens with periods. Group names get changed which leads to incorrect merging.
Your document says [here](https://github.com/nf-core/atacseq/blob/master/docs/usage.md#--narrow_peak): > MACS2 is run by default with the --broad flag. However, MACS2 document says the opposite [here](https://github.com/macs3-project/MACS/blob/bce60cf0e523dba306b71644c8397341017e0663/bin/macs3): > --broad > If set, MACS will try to...
Hi, All, I have been trapped by a problem which I found that one condition of my data has signals always higher than the other. I discovered this phenomenon by...
Hello there, As usual, I am so glad I can run your pipeline for our clients! :-) This time around, I found some irregularities in the MultiQC report, and just...
Hi, I struggle to understand whats happening. I am running the pipeline from cloned github repo since I may need to adjust and implement a few aditional steps. The design.csv...
I come across a problem when apply this pipeline to mu ATAC-Seq data. The error is: ``` [7c/09c5ba] process > CHECK_DESIGN (design_pe.csv) [100%] 1 of 1 ✔ [b4/ee799a] process >...
Currently no matter what you set $TMPDIR to the macs2 callpeak commands (MERGED_LIB_MACS2, MERGED_REP_MACS2) ignore this and write temporary files to /tmp. On some HPC this causes issues. The modification...
In the MultiQC report, only one of the samples appears in the following sections: - MERGED LIB: PICARD - MERGED LIB: deepTools: Read Distribution Profile after Annotation - MERGED LIB:...