View source for 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:
# The FASTQ file is verified for correct format.
# [http://code.google.com/p/cutadapt/ CutAdapt] is run to trim adapter sequence from the reads (parameters:  -q 25 --quality-base=64  -m 17)
# [http://research-pub.gene.com/gmap/ GMAP] is run to index the reference genome sequence.
# [http://research-pub.gene.com/gmap/ GSNAP] is run to align the reads to the reference sequence.
# [http://samtools.sourceforge.net/ SAMtools] is run to compute per-position read depth of the resulting alignment.
# [http://cufflinks.cbcb.umd.edu/ Cufflinks] is run to compte per-transcript FPKM.
# The three results (raw alignment, per-position read depth, and per-transcript FPKM) are loaded as separate [[Experiments]] into a [[Notebook]].