Weisheng Wu

So far it didn't cause any issue. Just hope it could keep the consistency unless there is a reason for it...

Thanks!

@wdecoster Good point. I do have a complicated case here. I actually included a transgene in the reference for alignment and the transgene is 100% identical to its endogenous copy...

Sorry I don't know the answer to your question. I'd like to look into it if I can make bis-snp work. Currently I can't get through the recalibration step due...

@FleurGaBru Thanks for posting your solution. My concern, however, is that BaseRecalibrator is blind to the C->T bisulfite conversion. The default behavior of GATK recalibration is to assume all mismatches...

I have the same problem here. And many other people have reported this bug. One solution is to use the old version of the cistarget files: https://github.com/aertslab/SCENIC/issues/379 Rolling back to...

What kind of GPU differences can cause this irreproducibility? I have these GPU nodes in the cluster I use: - 2x NVIDIA Tesla V100 16GB - 3x NVIDIA V100 16GB...

Thanks. I ran the filtering as shown in the SCENIC vignette (R version) to filter the genes and used the kept genes for pyscenic: ``` genesKept

Thanks for replying quickly. The .cnr, .cns and the vcf files can be downloaded here: https://usegalaxy.org/u/mapped%20reads%20in%20illumina%2011/h/cnvkitdata The vcf contains the variants called by GATK HaplotypeCaller from tumor and normal samples...

@jtamames I tried it. The log says: ``` Calculating coverage for functions Reading coverage in /nfs/mm-isilon/bioinfcore/ActiveProjects/weishwu/test/coassembly_with_drepGenomes/intermediate/10.coassembly_with_drepGenomes.mapcount Reading rpkm in /nfs/mm-isilon/bioinfcore/ActiveProjects/weishwu/test/coassembly_with_drepGenomes/intermediate/10.coassembly_with_drepGenomes.mapcount ``` The job finished, but the file "10.coassembly_with_drepGenomes.mapcount" is actually...