Delaney Sullivan
Delaney Sullivan
Those errors are due to files not being found. This doesn't appear to be an issue with kallisto; it's an issue with the script that you tried to run.
You'll need to show the exact commands you're running otherwise there's no way anyone can help you (we don't have access to your computer or server).
HDF5 is not really being phased out -- it's just a pain to deal with that file structure and all the issues (including compilation issues) associated with it, but I...
Amazing! Thanks for your contribution toward installing kallisto from source -- for htslib, I'm planning/hoping to make it an optional cmake option in the future, since it's been giving trouble...
getting 'Segmentation fault' while writing pseudoalignments to BAM format in kallisto version 0.50.1
Pseudobam files are not supported in versions 50+
getting 'Segmentation fault' while writing pseudoalignments to BAM format in kallisto version 0.50.1
bias is not supported either (and even in older versions of kallisto, we don’t really recommend bias)
Yes, it should work -- the main issue is that the index structure will be different (so any index you generate with the current version of kallisto will not be...
Ooh ok, good to know — thanks. I thought I had a newer version of Bifrost working with kallisto at some point but it was two or so years ago...
Are you using cm with bustools count or kallisto bus?