Cuffmerge
Cuffmerge takes all cufflinks results to be compared and creates a global file required for cuffdiff. A list of all 'transcripts.gtf' cufflinks files to be merged is first created and named 'assemblies.txt'
# a typical cuffmerge command.
cuffmerge -p 8 -g mm9.ensgene.gff -s mm9.fa -o merged_asm assemblies.txt
In this example, 8 threads max are attributed to the job (-p), the reference exome (-g) is set to the mm9.ensgene.gff file (obtained from UCSC tables and comverted using ), the mouse full reference genome in provided in fasta format (mm9.fa, -s), the last two arguments define the name for the output (-o) and the list of input files.
The result will be a new folder named 'name_clout' and containing several files describing the result of mapping the reads to the ensgene exome.
-rwxrwx---. 1 root vboxsf 4.6M Nov 7 14:37 genes.fpkm_tracking -rwxrwx---. 1 root vboxsf 14M Nov 7 14:37 isoforms.fpkm_trackingd rwxrwx---. 1 root vboxsf 4.0K Nov 5 14:27 logs -rwxrwx---. 1 root vboxsf 219M Nov 7 14:39 merged.gtf -rwxrwx---. 1 root vboxsf 0 Nov 7 14:34 skipped.gtf -rwxrwx---. 1 root vboxsf 212M Nov 7 14:37 transcripts.gtf
The obtained folder is the input for the cuffdiff command.
