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                                            Delaney Sullivan

Lamanno workflow with SMARTSEQ2 data

First, remove -w NONE Second, lamanno is the old workflow; to use it, you might want to try installing kb-python version 0.27.3 or earlier if the current version doesn’t work.

Lamanno workflow with SMARTSEQ2 data

You could just use -x BULK

[~warn] Warning, zero reads pseudoaligned check your input files and index,

There is nothing wrong. Your sequencing data simply does not have that gene in it.

Kallisto RNA velocity indices

You probably need more memory. Also, for that RNA velocity workflow, please downgrade to kallisto version 0.48

Kallisto RNA velocity indices

You need to make a new kallisto index (version48 and version51 of kallisto use different indices),