HMMRATAC
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HMMRATAC peak caller for ATAC-seq data
Dear all, I am trying to run HMMRATAC algorithm on bam files generated from ATAC-Seq data using: " java -jar HMMRATAC_V1.2.10_exe.jar -b data470.bam -i data470.bam.bai -g hg19.chrom.sizes.txt " command. However,...
Hey, I noticed you mentioned in HMMR paper that you uesd a 'in-house script' to transform the paired-end bam file to single-end bed files as the input of F-seq. I...
Hey, I am using hmmr and I encountered some problems. when I use the default syntax (java -jar HMMRATAC_V1.2.4_exe.jar -b ATACseq.sorted.bam -i ATACseq.sorted.bam.bai -g genome.info), it works good. but when...
I am running HMMRATAC Version 1.2.10-0 from conda installed into singularity image with conda 3 base. Trying to call peaks on mm10 based data. Here is the command that is...
I got the "java.lang.OutOfMemoryError" no matter what settings I used or how much RAM I have. I installed HMMRATAC using "conda install -c bioconda hmmratac". Below is my RAM and...
I work with Drosophila data; I used to call peaks using unshifted bam, recently, I tried shifted bam. The shifted bam is calling more peaks than unshifted, for example. |Samples|Shifted|Unshifted|...
If it is a non-human species，How to set the m parameter？
**Describe the bug** Some peaks in *.gappedPeak overlap. **To Reproduce** The following two peaks overlap in example output `65283_chr22_peaks.gappedPeak`: ``` chr22 37484220 37485340 chr22 37485300 37487330 ``` **Expected behavior** I...
**Describe the problem** Hi thanks for this tool! I got very low number (~200) of peaks for each sample by hmmratac compared with the number of those peaks (~2000) called...
Hi there I'm running HMMRATAC_V1.2.10_exe.jar to call peak for ATAC data. I have 4 replicates so I merged, sorted and indexed bam file and then went to call peak by...
