feature_type Key Error about cellbender HOT 7 CLOSED

What is the format of your input data? Is it CellRanger? MTX or h5?

from cellbender.

MTX. It's not from cellranger but has the same format. I hadn't had issues with it before recent commits.

from cellbender.

Yes, so I have been updating the data parsers to retain gene_name and gene_id info, as well as feature_type info (if it's 10x Genomics v3 chemistry + ). But I still want it to work in the case that data is not available. Can you post the result of

$ head genes.tsv

on your input file?

from cellbender.

I've gone with cellranger 3 format, results of zcat features.tsv.gz | head are:

ENSG00000251841.1 RNU6-1334P Gene Expression
ENSG00000184895.8 SRY Gene Expression
ENSG00000237659.1 RNASEH2CP1 Gene Expression
ENSG00000232195.1 TOMM22P2 Gene Expression
ENSG00000286130.1 AC006040.1 Gene Expression
ENSG00000129824.16 RPS4Y1 Gene Expression
CATG00000115038.1 CATG00000115038.1 Gene Expression
ENSG00000227289.2 HSFY3P Gene Expression
ENSG00000229163.2 NAP1L1P2 Gene Expression
CATG00000115039.1 CATG00000115039.1 Gene Expression

from cellbender.

Is it tab \t delimited? Or are those spaces?

from cellbender.

They are tabs, just doesn't present well in this format...

from cellbender.

Hmm, okay, I see what happened. I think you were unlucky enough to pull the branch as I was in the middle of updating things. There was a typo of 'feature_type' instead of 'feature_types'. This should be fixed in the branch as it currently stands. Give that a try.

... the perils of working with a branch under development! :) But I am happy to be getting your feedback.

from cellbender.