I am trying to use cufflinks-2.2.1.Linux_x86_64 for differential gene and expression analysis. First I used cufflinks with following command and got output files including transcripts.gtf. However, once I use cuffmerge I am getting an error. I am not sure if I installed it properly. please advice...
cufflinks ../sorted-SRR8136652.bam -o ../SRR8136652-cuff2.out
./cuffmerge -g ../Sus_scrofa.Sscrofa11.1.100.chr.gtf -s ../Sus_scrofa.Sscrofa10.2.dna.toplevel.fa -p 8 ../assemblies.txt
File "/usr/bin/cuffmerge", line 95 except getopt.error, msg: ^ SyntaxError: invalid syntax