Hi everyone,
I am trying to create a reference library using the following code:
STAR \
--runMode genomeGenerate \
--runThreadN 8 \
--genomeDir /scratch/c.c22019143/R256/fastq/Mapping/STAR/ \
--genomeFastaFiles /scratch/c.c22019143/R256/fastq/Mapping/STAR/Mus_musculus.GRCm39.dna_sm.primary_assembly.fa \
--sjdbGTFfile /scratch/c.c22019143/R256/fastq/Mapping/STAR/Mus_musculus.GRCm39.108.gtf
But I keep getting this error:
FATAL error, could not open file pGe.sjdbGTFfile=/scratch/c.c22019143/R256/fastq/Mapping/STAR/Mus_musculus.GRCm39.108.gtf
I downloaded the .gtf file from ensembl thrice to ensure I get the correct file. Could you please help?
Many thanks,
Niharika.