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Hi there, this is a bit of a shot in the dark, but I'm trying to wrap my head around analyzing broadPeak chip-seq files and stumbled across this repo. The approach described in https://github.com/resk…
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- ChIP-Seq from own data
- ChIP-Seq SKNBE2
- ChIP-Seq Schödel
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Jensen-Shannon Distance (JSD) plot
use deeptools npz output as input to jsd
encode: https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/master/src/encode_task_jsd.py
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# About
Let's rename the `Input` column to `Input_Control` and make it an optional column (for ATAC-seq). The name `Input` for ChIP samples could causes some confusion for users who are not experie…
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Create a workflow for peak calling VISION ChIP-seq datasets that (as closely as possible) matches the ENCODE best practices pipelines. ENCODE pipelines are [here](https://github.com/ENCODE-DCC/chip-se…
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It is not clear from docs if pileup support chip-seq tracks (narrow/broad peaks files). If yes, then it would be nice to see an example if no, then it would nice to know if the feature is in plans?
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IWC already contains a sufficient number of workflows that can be readily used for BRC purposes. We need to understands:
- understand which categories of workflows we have
- based on these categories…
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This paper looks really nice: https://doi.org/10.1093/nar/gkad1225
Has ChIP-seq, ATAC-seq, RNA-seq, enough replicates, two groups (for differential binding).
SRA: https://www.ncbi.nlm.nih.gov/b…
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Hi Cass!
the last time we checked the results there were something wrong the piks on IGV didn't corrispond to the list of genes in the excel file can u have a look? thanks
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```
The ChIP-seq wiggle output does not look publication quality. The reason is
because it is only plotted at 50bp windows, which is not high enough
resolution. We could simply change this to 10 or…