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Posts by mlweilert
Comment: C: ChIP-nexus peak call
... In addition, it is possible to boost your MACS2 peak call on exo/nexus data by running `macs2 callpeak –g dm –keep-dup=all –call-summits --ext-size 150 --shift -75`. By extending the fragment sizes and then recentering them, you are in a sense simulating ChIP-seq data. However, keep in mind that if ...
... Your problem lies with the line: gr1 = with(x1, GRanges(chr, IRanges(start=start, end=stop))) You are inputting a data.frame object into this command and relying on some assumptions. Check the header information on your data.frame object and make sure the data.frame column names match up to wh ...
Answer: A: ChIP-nexus peak call
... In addition to the answer by Satyajeet Khare, there are two other papers published on this information: [PeakXus] and [QNexus]. Each has their own strengths and weaknesses, so it is a good idea to read the associated papers carefully. Additionally, ChIP-nexus data provides strand-specific in ...
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