genomeGenerate with sjdb file mus muscular

[GoogleCodeExporter]

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

Original issue reported on code.google.com by olivier....@gmail.com on 12 Sep 2013 at 11:52

[GoogleCodeExporter]

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

Original comment by adobin@gmail.com on 24 Sep 2013 at 7:26