I'm trying to generate a custom genome using the provided sjdb file by running this:

"$star_Path --runMode genomeGenerate --genomeDir $star_genome_dir --genomeFastaFiles $genomeFastaFiles --runThreadN 8 --sjdbFileChrStartEnd $sjdbOverhangFile --sjdbOverhang 91"

I'm using the mm9.fa and the Mus_musculus.NCBIM37.66.gtf.sjdb file both provided under genome downloads, however this is the output:

EXITING because of FATAL error, the sjdb chromosome Y is not found among the genomic chromosomes SOLUTION: fix your file sjdbFileChrStartEnd=...../Mus_musculus.NCBIM37.66.gtf.sjdb_OG.txt at line #1

What is wrong?

Olivier

Hi Olivier,

this issue is caused by the different naming of chromosomes in mm9.fa (chromosomes' names start with 'chr') and Mus_musculus.NCBIM37.66.gtf.sjdb (chromosomes' names do not contain 'chr'). You would need to synchronize the naming of chromosomes in two files. Please ask your questions at https://groups.google.com/forum/#!forum/rna-star for a quicker response.

Cheers Alex