Search results

Q: Using peak summits for footprinting/TF binding motif analysis ? Do they need to be shifted ?

General Question

Status: Open.

#109 In LiuLabUB/HMMRATAC;

· eggrandio opened on Oct 24, 2024

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.

General Question

Status: Open.

#108 In LiuLabUB/HMMRATAC;

· ijeomameremikwu opened on May 29, 2024

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!

General Question

Status: Open.

#107 In LiuLabUB/HMMRATAC;

· dulcirena opened on Feb 9, 2024

Q: gappedPeak file visualization in IGV and interpretation

General Question

Status: Open.

#105 In LiuLabUB/HMMRATAC;

· olechnwin opened on Aug 22, 2023

Q: Removing duplicates with HMMRATAC

General Question

Status: Open.

#104 In LiuLabUB/HMMRATAC;

· tamuanand opened on Aug 6, 2023

Why the 4th column of bedgraph file values are E0, E1 and E2? What is the meaning of these values?

General Question

Status: Open.

#102 In LiuLabUB/HMMRATAC;

· danli349 opened on Jul 3, 2023

Q: Gold standard files to benchmark peak callers

General Question

Status: Open.

#101 In LiuLabUB/HMMRATAC;

· SuzonM opened on May 2, 2023

Exception in thread "main" java.util.InputMismatchException

Bug Report

Status: Open.

#100 In LiuLabUB/HMMRATAC;

· danli349 opened on Dec 2, 2022

genome.info is created with 0 bytes

Bug Report

Status: Open.

#99 In LiuLabUB/HMMRATAC;

· MariusHoh opened on Sep 26, 2022

background noise too high for my data?

General Question

Status: Open.

#98 In LiuLabUB/HMMRATAC;

· zmz1988 opened on May 16, 2022

BR: HMMRATAC fails to run on large genomes needing .csi index

Bug Report

Status: Open.

#96 In LiuLabUB/HMMRATAC;

· TeiturAK opened on May 1, 2022

FR: Return NFR-, mono-, di-, and tri-nucleosome signal tracks

Feature Request

Status: Open.

#95 In LiuLabUB/HMMRATAC;

· ccrobertson opened on Apr 12, 2022