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nf-core / atacseq

ATAC-seq peak-calling and QC analysis pipeline
https://nf-co.re/atacseq
MIT License
179 stars 116 forks source link

Add IDR analysis #36

Open drpatelh opened 5 years ago

drpatelh commented 5 years ago

Would be nice to add the IDR analysis that is currently carried out by the ENCODE pipelines: https://github.com/kundajelab/atac-seq-pipeline https://docs.google.com/document/d/1f0Cm4vRyDQDu0bMehHD7P7KOMxTOP-HiNoIvL1VcBt8/edit

Another implementation in NF: https://github.com/DoaneAS/atacflow

ENCODE ATAC-seq Guidelines: https://www.encodeproject.org/atac-seq/

Amongst other things, this will probably also involve creating pseudo-replicates by merging and equally sampling alignments across replicates.

drpatelh commented 5 years ago

As it stands bioconda::idr and bioconda::macs2 wont build in the same environment because they are built with Python 3 and Python 2, respectively.

https://anaconda.org/bioconda/idr/files

https://anaconda.org/bioconda/macs2/files

Need a workaround for this.

ewels commented 5 years ago

MACS2 Python3 support is hopefully coming... https://github.com/taoliu/MACS/issues/242#issuecomment-432829877 (though there have been threads around this since 2017, so not sure when..)