Cufflinks is a transcript assembly program for RNA-Seq data and it also provides transcript quantification and tools for identifying differentially expressed transcripts.
Cufflinks 1.3.0 is installed at /opt/ and the executable is located at /usr/local/genome/bin/
Basic cufflinks command:
cufflinks accepted_hits.bam -G <gtffile> -o <outputdirectory> &>cufflinks.log &
Input:
accepted_hits.bam : bam file produced by tophat
gtffile : gtf file with transcript information
outputdirectory: Directory to place output files in
Example: For human (hg19)
cufflinks accepted_hits.bam -G /home/daras/data/hg19/refFlat.cufflinks.2.exonsonly.gtf -o geneexp1_output &>cufflinks.log &
/home/daras/data/hg19/refFlat.cufflinks.2.exonsonly.gtf is a human (hg19) refFlat file that has been parsed into a gtf file that is acceptable by cufflinks.