Expression Analysis Pipeline: Difference between revisions
Jump to navigation
Jump to search
No edit summary |
No edit summary |
||
| Line 1: | Line 1: | ||
CoGe can generate gene/transcript expression measurements given a FASTQ input and an annotated genome. | CoGe can generate gene/transcript expression measurements given a FASTQ input and an annotated genome. Thanks to [http://www.skraelingmountain.com/ James Schable] 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: | When a FASTQ file of sequence reads is loaded in [[LoadExperiment]] and associated with an annotated genome, the following analysis steps are performed: | ||
| Line 10: | Line 10: | ||
# The per-position read depth and per-transcript FPKM values are log transformed and normalized between 0 and 1 for loading. | # 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]]. | # 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 [http://qteller.com/ qTeller]. | |||
TBD: how to do this ... | |||
Revision as of 18:21, 27 February 2014
CoGe can generate gene/transcript expression measurements given a FASTQ input and an annotated genome. Thanks to James Schable 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: --nthreads=32 -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 ...