Cufflinks error

[ameyer]

Hi,
I'm having a problem getting Cufflinks to run.
I used TopHat to align my reads but when running Cufflinks it gives the error:
Error: sort order of reads in BAMs must be the same.
I've tried converting the .bam file to .sam and it still gave the error so I then used the sort command given in the Cufflinks manual (sort -k 3,3 -k 4,4n accepted_hits.sam > hits.sam.sorted) but it still gave the error.
Why is it doing this?
Thanks

[jtrivino]

Hi

I use
samtools sort *.bam *_sort.bam
samtools index sort.bam