Delaney Sullivan
Delaney Sullivan
cds_from_genomic.fasta is not the whole genome; it's just the CDS. You need to supply a whole genome FASTA.
It builds an index from coding sequences; that doesn’t mean you supply the coding sequences. kb ref extracts the coding sequences for you from the genomic FASTA. That’s why the...
Most likely kallisto was compiled without hdf5 support. Also, which version of kallisto are you using?
It’s not about dependencies; kallisto needs to be instructed to be compiled with hdf5 support when you run cmake (you need to supply -DUSE_HDF5=ON)
Just recreate the index and run it with the same version of kallisto you used to create the index. I apologize for the oversight in not giving a better error...
Conda was having some issues — it kept editing the kallisto binary files whenever a new version of kb-python was uploaded. This caused the “conda kallisto binary” to be incompatible...
This means your GTF file is malformatted.
Yes, 63 for index k-mer size. And you can use --long and --platform=ONT when running pseudoalignment.
See our manual (being actively updated, so still a work-in-progress) here: https://github.com/Yenaled/kallisto-website RNA velocity requires nac, nac can be used for standard gene expression analysis, BAM is never used for...