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Homer's findPeaks: normalized Tag counts, Peak Score, and RPKMs
written by frI was reading [this](https://www.biostars.org/p/278730/) and [this](https://www.biostars.org/p/326797/) posts where it is mentioned that > normalized tag count [is] (equal to RPKM reflecting peak density). But I …
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HOMER annotatePeak -ghist --- lose of peaks?
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HOMER annotatePeaks.pl 'Unique Peak ID' in first column changed in output file
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HOMER annotatePeaks.pl problem
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Strand information when doing peak annotation with HOMER
written by jiab •As far as I can tell (by running tests manually), `annotatePeaks.pl` in the HOMER package [1] ignores strand information when searching the Transcription Start Site …
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read density plot in R
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Annotation bug using HOMER
written by pinky_pinkpinky •Dear Users, I am getting the below mentioned issue while executing annotatePeaks.pl using HOMER. ``` readline() on closed filehandle IN at /data/ngs/projects/Abhi/HOMER/bin/parseGTF.pl line 77. readline() …
