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Title: Issues · LiuLabUB/HMMRATAC · GitHub

Open Graph Title: Issues · LiuLabUB/HMMRATAC

X Title: Issues · LiuLabUB/HMMRATAC

Description: HMMRATAC peak caller for ATAC-seq data. Contribute to LiuLabUB/HMMRATAC development by creating an account on GitHub.

Open Graph Description: HMMRATAC peak caller for ATAC-seq data. Contribute to LiuLabUB/HMMRATAC development by creating an account on GitHub.

X Description: HMMRATAC peak caller for ATAC-seq data. Contribute to LiuLabUB/HMMRATAC development by creating an account on GitHub.

Opengraph URL: https://github.com/LiuLabUB/HMMRATAC

X: @github

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Q: Using peak summits for footprinting/TF binding motif analysis ? Do they need to be shifted ?https://github.com/LiuLabUB/HMMRATAC/issues/109
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
eggrandiohttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Aeggrandio
Q: How is the fourth column calculated for the digested_short.bdg, digested_mono.bdg, digested_di.bdg, and digested_tri.bdg output files when using the the flag --digested.https://github.com/LiuLabUB/HMMRATAC/issues/108
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
ijeomameremikwuhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Aijeomameremikwu
Q: I am working with a small genome (34 Mb) and I would like to ask for your advice on how to tune the default parameters. For instance, I thought it would make sense to change the window size (--window) and the maximum number of training regions to use during model building (--maxTrain). Thanks!https://github.com/LiuLabUB/HMMRATAC/issues/107
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
dulcirenahttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Adulcirena
Q: gappedPeak file visualization in IGV and interpretationhttps://github.com/LiuLabUB/HMMRATAC/issues/105
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
olechnwinhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Aolechnwin
Q: Removing duplicates with HMMRATAChttps://github.com/LiuLabUB/HMMRATAC/issues/104
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
tamuanandhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Atamuanand
Why the 4th column of bedgraph file values are E0, E1 and E2? What is the meaning of these values?https://github.com/LiuLabUB/HMMRATAC/issues/102
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
danli349https://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Adanli349
Q: Gold standard files to benchmark peak callershttps://github.com/LiuLabUB/HMMRATAC/issues/101
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
SuzonMhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3ASuzonM
Exception in thread "main" java.util.InputMismatchExceptionhttps://github.com/LiuLabUB/HMMRATAC/issues/100
Bug Reporthttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Bug%20Report%22
danli349https://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Adanli349
genome.info is created with 0 byteshttps://github.com/LiuLabUB/HMMRATAC/issues/99
Bug Reporthttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Bug%20Report%22
MariusHohhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3AMariusHoh
background noise too high for my data?https://github.com/LiuLabUB/HMMRATAC/issues/98
General Questionhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22General%20Question%22
zmz1988https://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Azmz1988
BR: HMMRATAC fails to run on large genomes needing .csi index https://github.com/LiuLabUB/HMMRATAC/issues/96
Bug Reporthttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Bug%20Report%22
TeiturAKhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3ATeiturAK
FR: Return NFR-, mono-, di-, and tri-nucleosome signal trackshttps://github.com/LiuLabUB/HMMRATAC/issues/95
Feature Requesthttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22Feature%20Request%22
ccrobertsonhttps://github.com/LiuLabUB/HMMRATAC/issues?q=is%3Aissue%20state%3Aopen%20author%3Accrobertson
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