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 (parameters: --nthreads=32 -n 5 --format=sam -Q --gmap-mode=none --nofails).
5. SAMtools is run to compute per-position read depth of the resulting alignment (mpileup -D -Q 20).
6. Cufflinks is run to compte per-transcript FPKM (parameters: -p 24).
7. The three results (raw alignment, per-position read depth, and per-transcript FPKM) are loaded as separate Experiments into a Notebook.