CLIP-seq pipeline can process eCLIP data?

Pipelines CLIP
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Great work and amazing flow website, congrats everyone!

I am wondering if the nextflow CLIP-seq pipeline can also process eCLIP data (from fastq files to peak calling?)

Thanks,
Gregor

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Hi Gregor! Great to hear from you. The pipeline certainly can process eCLIP data. We are in the process of processing all ENCODE eCLIP now here → Flow (you can see its been uploaded but not yet run through our pipeline). If you have more details on the library structure I can help you further. For the ENCODE eCLIPs that are paired end, we use the first read, I did some testing and mapping paired end doesn’t improve any metrics in my hands. If you want to normalise by input then the current Flow.bio pipeline doesn’t have any options however I am currently updating nf-core/clipseq to v.2.0 and on the feat-2-0 branch there I implemented pureCLIP and normalisation by input so I’d recommend trying that. Feel free to email me if that’s easier charlotte.capitanchik@kcl.ac.uk.

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I should say, my goal is to have Flow.bio consistent with v2.0 on nf-core as soon as possible, it’s just a bit in transition at the moment.

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