Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
Step 1: Download Cufflinks
Step 2: Compile Cufflinks
# tar -zxvf cufflinks-2.1.1.tar.gz # cd cufflinks-2.1.1 # ./configure --prefix=/usr/local/cufflinks/ \ --with-boost=/usr/local/boost \ --with-eigen=/usr/local/include
# make # make install
Step 3: Testing the installation
Download the test data
# /usr/local/cufflinks/bin/cufflinks ./test_data.sam
You should see the following output:
[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). File ./test_data.sam doesn't appear to be a valid BAM file, trying SAM... [13:23:15] Inspecting reads and determining fragment length distribution. > Processed 1 loci. [*************************] 100% Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges. It is recommended that correct paramaters (--frag-len-mean and --frag-len-std-dev) be provided. > Map Properties: > Total Map Mass: 102.50 > Read Type: 75bp x 75bp > Fragment Length Distribution: Truncated Gaussian (default) > Estimated Mean: 200 > Estimated Std Dev: 80 [13:23:15] Assembling transcripts and estimating abundances. > Processed 1 loci. [*************************] 100%
Verify that the file transcripts.gtf is in the current directory and looks like this (your file will have GTF attributes, omitted here for clarity)
test_chromosome Cufflinks exon 53 250 1000 + . test_chromosome Cufflinks exon 351 400 1000 + . test_chromosome Cufflinks exon 501 550 1000 + .