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40 Open 65 Closed
40 Open 65 Closed
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Issues list

Q: Using peak summits for footprinting/TF binding motif analysis ? Do they need to be shifted ? General Question
#109 opened Oct 24, 2024 by eggrandio
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
#108 opened May 29, 2024 by ijeomameremikwu
1
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
#107 opened Feb 9, 2024 by dulcirena
Q: gappedPeak file visualization in IGV and interpretation General Question
#105 opened Aug 22, 2023 by olechnwin
Q: Removing duplicates with HMMRATAC General Question
#104 opened Aug 6, 2023 by tamuanand
Why the 4th column of bedgraph file values are E0, E1 and E2? What is the meaning of these values? General Question
#102 opened Jul 3, 2023 by danli349
1
Q: Gold standard files to benchmark peak callers General Question
#101 opened May 2, 2023 by SuzonM
2
Exception in thread "main" java.util.InputMismatchException Bug Report
#100 opened Dec 2, 2022 by danli349
genome.info is created with 0 bytes Bug Report
#99 opened Sep 26, 2022 by MariusHoh
background noise too high for my data? General Question
#98 opened May 16, 2022 by zmz1988
2
BR: HMMRATAC fails to run on large genomes needing .csi index Bug Report
#96 opened May 1, 2022 by TeiturAK
4
FR: Return NFR-, mono-, di-, and tri-nucleosome signal tracks Feature Request
#95 opened Apr 12, 2022 by ccrobertson
6
BinaryCodec error with HMMRATAC Bug Report
#93 opened Jan 10, 2022 by NazaninHosseinkhan
Q: In-house script for transforming paired-end bam to single-end bed file General Question
#92 opened Dec 7, 2021 by jamesc99
Q: Error when using bedgraph option： Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException General Question
#91 opened Nov 16, 2021 by jamesc99
1
Shifted bam calls more number of peaks than unshifted bam General Question
#90 opened Oct 7, 2021 by RadPa
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space (RAM 256GB, --window 25000, --maxTrain 500))
#89 opened Sep 26, 2021 by Lei-Guo
1
Using HMMRATAC with CSI indexes and large chromosome sizes General Question
#88 opened Aug 29, 2021 by diego-rt
2
FR: How to set the m parameter？ Feature Request
#87 opened May 29, 2021 by chenchen-eng
BR: HMMRATAC throws an exception when using samblaster-deduped bam file even with --removeDuplicates false Bug Report
#86 opened May 18, 2021 by omegahh
1
Q: Peaks are too long and peak number is low General Question
#85 opened Apr 27, 2021 by WJH58
3
BR: HMMRATAC doesn't run if samtools index made with multithreading Bug Report
#84 opened Mar 30, 2021 by pratarora
2
Q: GC overhead limit exceeded General Question
#83 opened Mar 22, 2021 by Kayla-Morrell
Q: please explain the layout of the model shown in .model General Question
#81 opened Dec 15, 2020 by IanCodes
1
BR: Bug Report
#79 opened Nov 19, 2020 by EllieDuan
12
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