I have set #1 of bam files that were generated with galaxy a year ago.
I have a new set #2 of bam files that I generated recently from new fastq data.
If I trying cuffdiff on only bam files from set #1, it works fine. And if I try running cuffdif on only bam files from set #2 that it also works fine.
However, when I try running cuffdiff with files from set #1 AND set #2, I get the error: “Error: sort order of reads in BAMs must be the same.”
I tried the SortSam tool to sort BAM files by coordinate order from from set #1 and set #2, but I still get the same error after I running cuffdiff with the sorted files.
When using cuffdiff, I use a mm9 gtf file downloaded from Shared Data → iGenomes → mm9 → genes.gtf . I also select perform bias correction and mm9 for the locally cached reference genome.
Cuffdiff works fine when with these settings when I run it with only bam files from set #1 or only from set #2. But if I try to run cuffdiff to compare bam files from set #1 and set #2, then it gives me that sorting error.
Any advice would be greatly appreciated. Thanks!