Creating a pre-mRNA GTF

Question

[abiuma]

I am trying to create pre mRNA reference for my snRNA data. This is my command

cellranger mkref --genome=mm10-2020-A_premrna \
                 --fasta=refdata-gex-mm10-2020-A/fasta/genome.fa \
                 --genes=mm10-2020-A.premrna.gtf

I start getting this error as soon as it starts to excute the command

Creating new reference folder at /home/users/umatha/yard/apps/cellranger-3.1.0/mm10-2020-A_premrnaa ...done

Writing genome FASTA file into reference folder... ...done

Computing hash of genome FASTA file... ...done

Indexing genome FASTA file... ...done

Writing genes GTF file into reference folder... Invalid number of columns in GTF line 1: /home/users/yard/apps/cellranger-3.1.0/cellranger-cs/3.1.0/bin

I am new to this. Can someone please help me fix this!

[GenoMax]

Initial error seems to be clear in that your GTF file may not be correctly formatted.

You may also want to contact 10x tech support. They are generally very good in responding. Any particular reason you are making your own indexes (I assume it is related to pre-mRNA part?).

[abiuma]

I am trying to generate a pre-mRNA reference package. I downloaded the mouse genome using this command curl -O https://cf.10xgenomics.com/supp/cell-exp/refdata-gex-mm10-2020-A.tar.gz Then I started preparing the reference package with the above command I mentioned in the query. How do I format my GTF file?

[GenoMax]

See if this 10x support link helps (may need to log in with 10x account). Instructions are for human should work for mouse.

[abiuma]

Thanks, I will check it :)