Expression Analysis Pipeline

CoGe can generate gene/transcript expression measurements given a FASTQ input and an annotated genome.

When a FASTQ file of sequence reads is loaded in LoadExperiment and associated with an annotated genome, the following analysis steps are performed:

1. The FASTQ file is verified for correct format.
2. CutAdapt is run to trim adapter sequence from the reads (parameters: -q 25 --quality-base=64 -m 17)
3. GMAP is run to index the reference genome sequence.
4. GSNAP is run to align the reads to the reference sequence.
5. SAMtools is run to compute per-position read depth of the resulting alignment.
6. Cufflinks is run to compte per-transcript FPKM.
7. The three results (raw alignment, per-position read depth, and per-transcript FPKM) are loaded as separate Experiments into a Notebook.