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.