HMMRATAC
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LiuLabUB
HMMRATAC peak caller for ATAC-seq data
Hi I was using HMMRATAC with the instructions provided, however, I found that the following error: Exception in thread "main" java.lang.RuntimeException: Invalid file header in BAM index This error has...
I found that when blacklist was included with -e blacklist, there was no Name_training.bed in the output, while when blacklist was not included, Name_traning.bed was generated in the output. Are...
**Describe the bug** I'm running HMMRATAC on several plant genomes which vary greatly in size. HMMRATAC fails when running on the largest genomes that require a .csi index. It produces...
**To Reproduce** the bam file has been sorted by `samtools sort` and deduplicated by `samblaster`. **Screenshots** **System (please complete the following information):** - OS: centos7 - JRE version: openJDK 8...
I'm working with an organism with a very large genome and thus I require the use of a CSI index. However, when I pass HMMRATAC my csi index, it complains...
The gradle action "Run command line test" is failing on the `feature-CICD` branch. It's error is: ``` Run java -jar ../build/libs/HMMRATAC-snapshot-exec.jar -b 65283_treat_rep1.chr22.bam -i 65283_treat_rep1.chr22.bam.bai -g hg19.chr22.genome -o Test2 --model...
Hello, thanks for the nice and user-friendly tool! I have atac-seq data (150 bp pair-end) from small plant genome, and have been trying HMMRATAC for a while. So the problem...
Thank you for this great tool! In addition to the inferred states, we are interested in using the signal tracks that HMMRATAC uses as input to the HMM algorithm for...
**Describe the bug** Setting `--modelonly true` is ignored. **To Reproduce** `java -jar HMMRATAC_V1.2.10_exe.jar -b 65283_treat_rep1.chr22.20to30MB.bam -i 65283_treat_rep1.chr22.20to30MB.bam.bai -g hg19.chr22.genome --modelonly true` **Expected behavior** I would expect HMMRATAC to quit after...
**Use case** Hello, I'm analysing some ATAC seq from different tissue and different samples of 5 instar butterflies. For some of the file the tool works properly but for some...
