Alex Predeus
Hello, I think it would be very helpful to make an option similar to -i option in mash: > -i Sketch individual sequences, rather than whole files, e.g. for >...
Hello, I was wondering if you considered adding genome options to dammit? I figured once there's gene models for the genome, it should be fairly easy to annotate the predicted...
When running dammit databases --install, I've ran into the error that seems to do with BUSCO files not being there anymore. Namely, curl http://busco.ezlab.org/files/metazoa_buscos.tar.gz generates nothing since there's no such...
Hi, two quick questions: 1) which version of `freebayes` and other tools are used in souporcell? I've installed freebayes independently (need to run just the variant calling command), and the...
Hello, I was wondering if you'd expect result asymmetry when running `shared_samples.py` on two samples with sample number of donors (2) in two different orders - e.g. sample 1 vs...
Dear velocyto team, I was wondering what exact command is used to identify the reads overlapping the repeats, when this option is used? There are few ways of doing it...
Hello, I was wondering about the annotation version you were using for processing mouse experiments using Kallisto. Ensembl 90 annotation has 131,195 unique transcripts; however, the cDNA file you've used...
Dear KrakenUniq team, I'm having an interesting issue that's quite obviously related to the temporary files, and that I'm not sure how to circumvent. Basically, I need to run many...
NH tag
I've searched for a while, but all I find is very old threads with many confused people, so I figured I will ask here. Apparently, bowtie2 and bwa do not...
Hello Ryan, I'm getting the same error with both the latest Bioconda version of Rebaler and the cloned latest version from repository. This is the part of the log where...