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maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
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Request: ATAC-seq pipeline for single-end sequencing #563

Closed AdrijaK closed 4 years ago

AdrijaK commented 4 years ago

Hi snakePipes, thank you for the great pipelines. I would like to ask if it is possible to add 'single strand' option to the ATAC-seq pipeline?

Inspiration: https://github.com/taoliu/MACS/issues/145 https://github.com/taoliu/MACS/issues/195

Thank you!

dpryan79 commented 4 years ago

Peak calling alone won’t produce reliable results. Determining fragment sizes is an important step since that determines what is likely to be histone and what is open chromatin. Since this information is lost with SE data we think it’s best to simply not do such analyses. In short, I think SE ATAC data is a waste of time to analyze.

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On 24. Feb 2020, at 11:52, Adrija Kalvisa notifications@github.com wrote:

 Hi snakePipes, thank you for the great pipelines. I would like to ask if it is possible to add 'single strand' option to the ATAC-seq pipeline?

Inspiration: taoliu/MACS#145 taoliu/MACS#195

Thank you!

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katsikora commented 4 years ago

Hi Adrija,

we indeed do not support single end sequencing reads in our ATACseq pipeline and we have no plans to change that.

We could provide a second mode for calling ATACseq peaks with MACS2, like we do for the ChIPseq workflow (-f BAM instead of -f BAMPE), but we would still require paired end reads to have a good estimate of fragment size.

AdrijaK commented 4 years ago

Thank you for the insight. Would you consider that it is impossible to call nucleosome free regions using SE ATACseq libraries?

katsikora commented 4 years ago

I don't think you can distinguish nucleosome (long fragments) from nucleosome-free (short fragments) signal in SE ATACseq, as you don't have the fragment size information. As Devon pointed out before.

AdrijaK commented 4 years ago

Thanks. Although you cannot distinguish between nucleosome-free regions and nucleosome regions using SE ATACseq, can you still identify "open chromatin" regions?

dpryan79 commented 4 years ago

Yes, but then you can't do peak calling and might as well just sequence whole genome DNA, since that will also bias toward open chromatin. SE ATAC-seq is a waste of money and resources.