Hi I'm new to RNA-Seq analysis. I ran the following command with cuffdiff: cuffdiff -o /home/silicon/mouse/diff_out -b /home/silicon/mouse/GRCm38/Sequence/Bowtie2Index/genome.fa -p 7 -L g1,g2 -u /home/silicon/mouse/assembly/merged_asm/merged.gtf, \ .//home/silicon/mouse/alignment/Tophat_S2/accepted_hits.bam, /home/silicon/mouse/alignment/samp12_alignment/accepted_hits.bam
and I got the following error: Warning: Could not connect to update server to verify current version. Please check at the Cufflinks website (http://cufflinks.cbcb.umd.edu). Error: cannot open reference GTF file /home/silicon/mouse/assembly/merged_asm/merged.gtf, for reading
Can anyone help me out?