[ensembl-dev] Custom GTF

[Pankaj Agarwal]

Hi,
I needed the human ERBB2 gene fasta formatted sequence and the corresponding GTF, which I downloaded from the Ensembl site.
Then I added these to the mouse ref fasta and gtf respectively and tried to build the index.
This is needed because I have a mouse tumor sequencing data that I am analyzing for a whole transcriptome RNAseq study and the human ERBB2 has been knocked-in.
I am getting the following error in the GTF format:

cellranger mkgtf \
> Mus_musculus.GRCm38.84.gtf \
> Mus_musculus.GRCm38.84.filtered.gtf \
> --attribute=gene_biotype:protein_coding \
> --attribute=gene_biotype:lincRNA \
> --attribute=gene_biotype:antisense
/GenomicPrimaryData/installs/10X/cellranger-2.2.0/cellranger-cs/2.2.0/bin
cellranger mkgtf (2.2.0)
Copyright (c) 2018 10x Genomics, Inc.  All rights reserved.
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Writing new genes GTF file (may take 10 minutes for a 1GB input GTF file)...
Property 'transcript_id' not found in GTF line 1591734: 17      Ensembl exon    39687834        39688057        .       -       .       Name=ENSE00003599710;Parent=ENST00000579146

Please fix your GTF and start again.

The line that is causing the problem is:
17      Ensembl exon    39687834        39688057        .       -       .       Name=ENSE00003599710;Parent=ENST00000579146

Can you please help with troubleshooting this problem.

Thanks,

- Pankaj

-----------------------------
Pankaj Agarwal, M.S
Bioinformatician
Data Analyst
Applied Therapeutics
Div. of Surgical Sciences
Dept. of Surgery
Duke University
M: 919-244-6389
O: 919-681-2251
p.agarwal at duke.edu<mailto:p.agarwal at duke.edu>

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