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

I am running Cufflinks for transcriptome assembly using the .bam file generated by Hisat2. I tried both bam and sorted bam files

cufflinks --no-update-check -o ./ -p 15 accepted_hits.bam


it gives the following error:

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


UPDATE: It is working fine now. It seems there were some issues with the reference file. The BAM files generated from Tophat2 also gave the same error. I downloaded the updated reference file and it worked great.

• Maybe post some code so that we can follow what you're doing?
– benn
Apr 3 '18 at 11:00
• Hello again, could you please add also the Hisat2 command? We are really trying to help, but to do that, we need more info. (do not hesitate to write there everything you tried) Apr 4 '18 at 8:38
• Instead of an update the preferred method would be to create an answer and then accept it. Apr 6 '18 at 18:31

Just add --dta-cufflinks to your Hisat2 command, so that the output alignment file provides the attributes needed by Cufflinks (XS flags). This should do the job.