Different ways to identify gtf format between version 7.0.0 and 7.2.0 of Cellranger

[lexuziandyu]

Hi, recently when I was using the cellranger count command, I encountered an intresting problem. I used the mkref command (version 7.2.0) to build a 10x genome of macaca mulatta , using "GCF_003339765.1_Mmul_10_genomic.fna" and "genomic.gtf" files. It was just fine to run the following steps using version 7.0.0, but when I changed to 7.2.0, I got the error info below, using the same pre-built genome: Parsing GTF on line 840: source: cannot contain spaces The line is like: Line = 'NC_041754.1 Curated Genomic gene 1747947 1748243 . + . gene_id "MACMULV1R-PS1002"; db_xref "GeneID:100312438"; description "vomeronasal 1 receptor macMulV1R-ps1002 pseudogene"; gbkey "Gene"; gene "MACMULV1R-PS1002"; gene_biotype "pseudogene"; pseudo "true";' Here's my command: cellranger count --id=x \ --transcriptome=~/ref/macaca_mulatta_NCBI \ --fastqs=~/fastqs \ --sample=sample1 \ --localcores=16 \ --include-introns=false \ --nosecondary \ --disable-ui I would really appreciate if you could help me to solve thsi problem. Thx!

[lilyle84]

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