I generated SAM files using GSNAP. Sorted them using the following command:
sort -k 3,3 -k 4,4n identifier.unpaired_uniq > file
Now, I'm able to run cufflinks but when I run cuffdiff, it says:
([bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). [17:10:05] Loading reference annotation. [17:10:08] Inspecting maps and determining fragment length distributions.)
And then keeps running. It's been days but it is still running. Here is the cuffdiff command:
cuffdiff merged_asm/merged.gtf P1_02.uniq.sorted,P2_02.uniq.sorted Control_P1_12.uniq.sorted,Control_P2_12.uniq.sorted,Control_P1_13.uniq.sorted,Control_P2_13.uniq.sorted -o diff_out.P_02vsContol -p 8 -L P,Control
Can someone point out where I'm going wrong?