i am trying to run cufflinks over Bam files that generated through Tophat but i get the sort order error. i lookup for other posts with this topic but they were not that much useful. I try to solve it by Samtools sort with option -n and also without it but it doesn't work. i also check the header of the Bam files they were the same :
@HD VN:1.0 SO:coordinate
The transcript that i use is :
./cuffdiff -o cuffdiff_output \ -b /home/alihkz/References/Trasncriptome/gencode.v19.annotation.fa \ -p 8 \ -L pre,pro \ -u ./Homo_sapiens.GRCh37.87.chr.gtf \ /home/alihkz/bam/high/sample25.bam \ /home/alihkz/bam/high/sample26.bam
can some one clarify what's the source of my error?
Thanks for any comments in advance.