Difference between revisions of "Expression Analysis Pipeline"
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When a FASTQ file of sequence reads is loaded in [[LoadExperiment]] and associated with an annotated genome, the following analysis steps are performed: | 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. | # The FASTQ file is verified for correct format. | ||
| − | # [ | + | # [http://code.google.com/p/cutadapt/ CutAdapt] is run to trim adapter sequence from the reads. |
# [http://research-pub.gene.com/gmap/ GMAP] is run to index the reference genome sequence. | # [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://research-pub.gene.com/gmap/ GSNAP] is run to align the reads to the reference sequence. | ||
Revision as of 12:10, 27 February 2014
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.
- CutAdapt is run to trim adapter sequence from the reads.
- GMAP is run to index the reference genome sequence.
- GSNAP is run to align the reads to the reference sequence.
- SAMtools is run to compute per-position read depth of the resulting alignment.
- 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.
