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pachterlab / kb_python

A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
https://www.kallistobus.tools/
BSD 2-Clause "Simplified" License
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kb ref prebuilt indices #197

Closed ryanz8 closed 1 year ago

ryanz8 commented 1 year ago

Hi, kb ref provides prebuilt indices with the -d flag:

  -d {human,mouse,linnarsson}
                        Download a pre-built kallisto index (along with all
                        necessary files) instead of building it locally

However, I haven't been able to find anywhere a description of these indices or how they were built.

I would appreciate any information or documentation that sheds some light on this. Thanks!

Yenaled commented 1 year ago

Don't use the prebuilt indices -- they haven't been updated in a while and are outdated. I strongly recommend generating your own index.

You can view the cDNA FASTA and transcripts-to-gene map for the prebuilt index; if you want to reproduce generating it, I'm afraid it was generated by an older version of kb-python (hence outdated). Just generate your own index . We'll update+document the prebuilt indices once our next version of kallisto is out (this summer).

ryanz8 commented 1 year ago

Understood, thanks for the response!