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bcbio / bcbio-nextgen

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
https://bcbio-nextgen.readthedocs.io
MIT License
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SICER2 support #3073

Closed mjsteinbaugh closed 4 years ago

mjsteinbaugh commented 4 years ago

Can we add SICER2 support for ChIP-seq peak calling?

I'm working on a bioconda recipe here: https://github.com/bioconda/bioconda-recipes/pull/20017

Here are some URLs with more details:

roryk commented 4 years ago

Heya, ENCODE uses MACS2 (https://github.com/ENCODE-DCC/chip-seq-pipeline2)-- is there a reason for wanting SICER2 over it?

mjsteinbaugh commented 4 years ago

We're using MACS2 primarily for peak calling but some vendors (e.g. ActiveMotif) are using SICER internally in their pipelines. I thought it might be a good idea to build in support, since it seems to be a popular alternative to MACS2. It's a good algorithm for H3K27me3 calling.

roryk commented 4 years ago

Gotcha, we're probably not going to do it unless its demonstrably better than MACS2 as it will add a bunch of support overhead.

mjsteinbaugh commented 4 years ago

No worries thanks Rory. We may just pipeline it out in Nextflow.

roryk commented 4 years ago

Thanks! It would be awesome to know if it performs better-- if you end up using it and it beats MACS2, let us know. Closing for now.

roryk commented 4 years ago

Are you using bowtie2 or bwa for your alignments?

mjsteinbaugh commented 4 years ago

bowtie2