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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.

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