Simone Maestri

Hi @passelma42, I'm facing the same issue too. Do you know why newer numpy versions are causing the issue? Is that due to the fact that they result in the...

Hi @passelma42 , in case you are still interested in the topic, I also wrote a Nextflow implementation of [longread_umi](https://github.com/SorenKarst/longread_umi) pipeline with some adjustments, named [UMInator](https://github.com/MaestSi/UMInator). Best, Simone

I have the following non-empty files: - bam.stub - bam.stub.config - start_sorted.bam.bedpe - a very large set of chr#1.chr#2.(+/-).(+/-); I think you mean these are all the discordant bams That's...

1020 chr chr +- files are written in total, some of them are empty but the majority is not. Yes, I already set ulimit -f to 16384 and tried running...

Yes, I'm running Hydra on a single sample. I had only one ~1GB bedpe file.

I am running them both, together with other 5 softwares (potentially) in the framework of SVE (https://github.com/TheJacksonLaboratory/SVE). If you tell me that is doesn't work with a single sample that's...

Just one more question. Does Hydra support hg38 reference? Because the BAM file I'm using has been obtained mapping fastq reads to hg38. Could that be the reason for the...

Hi, I think the issue could be due to the fact that, also in case you are not going to use fasta and tsv files (because you already imported them),...

Hi, I assume there may be an issue with the qza files you used. In particular, there may be a naming inconsistency for the two taxa AB116294 and AB116313. You...

I think you should be able to discard those entries in the fasta file with the following command: ``` seqtk seq -A dna-sequences.fasta | sed -e '/AB116313/,+1d' | sed -e...