cufflinks version 0.8.2 vs 0.8.3

[damiankao]

I ran 0.8.2 few months ago for a project and it worked fine on my .SAM files. After downloading 0.8.3, it started giving me a sort error.

I sorted my files exactly the same way as I did with 0.8.2. My .SAM file actually works with 0.8.2, but not 0.8.3. Is there something new with how it checks sorting in the new version? I noticed it was throwing me a sorting error based on reference contig name. Do I need to sort my .SAM file based on reference contig name and coordinates in the new version?

[john_mu]

If you use the sort command suggested by cufflinks

Something like this (it should be printed out when it gives the sorting error):
sort -k 3,3 -k 4,4n hits.sam > hits.sam.sorted

Then it will work

the (-k 3,3) indicates that the reference contig name must also be sorted.