[BioC] Quick question about Chromosome names using Tophat2 and Cufflinks w/Ensembl NCBIM37

[Sindre Lee]

Tophat2 cmd:

tophat2 -o path/to 
--transcriptome-index=/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Genes/genes 
/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bowtie2Index/genome 
001.fastq.gz

Cufflinks cmd:

cufflinks --output-dir path/to --GTF-guide 
/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Annotation/Archives/archive-2013-03-06-18-55-12/Genes/genes.gtf 
--frag-bias-correct 
/Mus_musculus_Ensembl_NCBIM37/Mus_musculus/Ensembl/NCBIM37/Sequence/Bowtie2Index/genome.fa 
--multi-read-correct --upper-quartile-norm --verbose accepted_hits.bam

Cufflinks then names the chromosomes like this, is that correct? How 
can I control this or alter it?

20: MT
10: 18
11: 19
4: 12
5: 13
2: 10
3: 11
8: 16
9: 17
6: 14
7: 15
22: Y
21: X
19: 9
18: 8
17: 7
16: 6
15: 5
14: 4
13: 3
12: 2
1: 1

Thank you!