Difference between revisions of "Expression Analysis Pipeline"
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Revision as of 10:26, 4 April 2014
CoGe can generate gene/transcript expression measurements given a FASTQ input and an annotated genome. Thanks to James Schnable, creator of qTeller, for help developing this pipeline!
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.
- CutAdapt is run to trim adapter sequence from the reads (parameters: -q 25 --quality-base=64 -m 17).
- GMAP is run to index the reference genome sequence.
- GSNAP is run to align the reads to the reference sequence (parameters: -n 5 --format=sam -Q --gmap-mode=none --nofails).
- SAMtools is run to compute per-position read depth of the resulting alignment (mpileup -D -Q 20).
- Cufflinks is run to compte per-transcript FPKM (parameters: -p 24).
- The per-position read depth and per-transcript FPKM values are log transformed and normalized between 0 and 1 for loading.
- The three results (raw alignment, per-position read depth, and per-transcript FPKM) are loaded as separate Experiments into a Notebook.
Genomes for which this analysis has been performed can have features imported into qTeller. TBD: how to do this ...
Video:
