atacseq
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nf-core
ATAC-seq peak-calling and QC analysis pipeline
Bug report for an edge case that I encountered. When the fasta option is given a glob, for example `--fasta 'genome/*'`, the `bwa_base` variable is set to `*` at [line...
Bug report for this error: ``` Channel `ch_gene_bed` has been used twice as an input by process `MERGED_LIB_PLOTPROFILE` and process `MAKE_TSS_BED` -- Check script 'nf-core/atacseq/main.nf' at line: 1023 ``` -...
Hi , after analysis, the comparison is control vs treatment, how I do make it treatment vs control if I need to run the pipeline again. Thank you! Best regards,...
Request for differential peak analysis. Basically, if you have two groups specified in your design file, you'd run a test of whether they peak overlap is significantly similar (e.g. by...
Reposting here from the [nf-core Slack](https://nf-co.re/join) for posterity. Thanks for @drpatelh for figuring this out! ## Problem nextflow/atacseq pipeline does not recognize the design.csv file, even though it follows the...
Hi, I was wondering if adding the feature of shifting and splitting the reads after the alignment would be helpful. A recent review on the approaches to analyze ATAC-seq data...
Another enhancement to the workflow would be to add the option to call peaks with Genrich: https://github.com/jsh58/Genrich Thank you!
Hi everyone, would it possible to make the specification of a GTF file optional? I am often working with non-model systems that do have an assembled genome but no gene...
Hi everybody, a nice feature would be to additionally have Hidden-Markow-Models as implemented in ChromstaR for genome-wide characterization of open chromatin landscape. The approach would be as described here: "On...
Would be good to have an optional limma implementation for the differential analysis that would be an alternative to using parallised DESeq2. See https://github.com/nf-core/atacseq/issues/79#issuecomment-586534337 cc @mikelove @kauralasoo @macroscian
