cufflinks error

[polsum]

Hi I am comparing two Bam files with cuffdiff but I get the following error.

Error: sort order of reads in BAMs must be the same

I use bowtie to produce sam files, convert them to bam and sort them with samtools.

I inspected the sam files and the order seems to be the same in both files. Not sure whats going on.

Can any one help? thanks in advance.

[cw11]

Maybe try aligning with Tophat? CuffDiff is designed to take Tophat output.

[polsum]

cw1

thanks. I copied the header lines of one file and pasted in the second file and then had no problems.