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Output files & filtering #1
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I would also like to know the answer to this. |
Yes - me too! Had a conference with @j-andrews7 about this earlier today. |
I also had this question. The end of |
Got the same question. Looking forward to the answer here. |
From the published paper supplementary figure 1 legend: After all test fragments have been filtered and/or collapsed into output peaks, two output files are produced: “optimal” for peaks p ≤ θ (where θ is the threshold suggested by the binomial test) and “all” containing all peaks regardless of p. https://ars.els-cdn.com/content/image/1-s2.0-S0888754321001531-mmc1.pdf |
is there any progress here with an answer? thx |
Hello,
thanks for putting this tool together.
Could you please elaborate on what exactly the output files are and how one would need to filter them?
In contrast to the README I get two files,
*_all.bed
and*_optimal.bed
(but not T1/T2).The command was simply
chipr -i rep1.narrowPeak rep2.narrowPeak -o out
for a normal transcription factor ChIP-seq.=> What is the "optimal" file here compared to "all"?
=> I am unsure how to obtain the final list of reproducible peaks (and from which file).
Do I filter any of these files based on FDR ($9)?
Since both files contain entries with FDR > 0.05 (with --alpha left at default 0.05), what is the relationship between FDR and alpha (if there is any), and when would it make sense to change alpha?
Edit: After playing with it, it appears that alpha has no effect on the output, can you clarify?
=> Also, the --fragment option, based on the preprint I guess it is recommended for TF ChIP-seq, is that correct?
=> WHat is the difference between "primary" and "secondary" peaks in the output?
Hope you can clarify, thank you for your time, and sorry for the wall of text.
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