Briefly, t2g.txt contains the transcripts-to-gene mappings, cdna_t2c.txt contains all the cDNA (spliced) transcripts, and intron_t2c.txt contains all the "intronic" (i.e. unspliced) transcripts.
nucleus is used for single-nucleus data while lamanno is used for RNA velocity. There are subtle differences between the two workflows (e.g. for nucleus, the spliced+unspliced matrices are added up while for RNA velocity, separate matrices are generated that can be fed directly into the velocyto workflow).
First of all thank you for openning this issue, it helped me better understand the nature of the command parameters. But here is my issue :
I am buiding a mouse index using kb ref with the following command line :
In my case, after running the kb ref, t2g.txt, cDNA_t2c.txt and introns_t2c.txt files are... EMPTY. As I look back at the kb --help, I understand that all of these parameters are supposed to be generated :
There is something very unclear to me, what could I be doing wrong ? How did you solve you problem GenoMax ?
Thanks in advance for your help
Please create a new question rather than posting this as an answer to an existing question.
Also, you cross-posted here: https://github.com/pachterlab/kallistobustools/issues/44
(and I answered there)