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Cufflinks convert the mapping results obtained from tophat in to per-exon counts based on the gene model selected during mapping.

# a typical cufflinks command.

cufflinks -q -p 8 -o name-clout name-thout/accepted_hits.bam

In this example, 8 threads max are attributed to the job, the terminal output is kept to a minimum (-q = quiet mode), and names are defined for the input and output folders.

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 1.5M Oct 24 17:35 genes.fpkm_tracking
-rwxrwx---. 1 root vboxsf 2.0M Oct 24 17:35 isoforms.fpkm_tracking
-rwxrwx---. 1 root vboxsf  162 Oct 24 17:52 skipped.gtf
-rwxrwx---. 1 root vboxsf  35M Oct 24 17:35 transcripts.gtf

When different conditions are represented by different sample groups, the next step is to compute differential expression by contrasting two or more groups. This can be done using cuffdiff, another command from the cufflinks package.

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