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RNA-seq Analysis
Overview
GenePattern offers a suite of tools to support a wide variety of RNA-seq analyses, including short-read mapping, identification of splice junctions, transcript and isoform detection, quantitation, and differential expression. The modules have been adapted from widely-used tools. GenePattern also provides pipelines that allow you to perform a number of multi-step RNA-seq analyses automatically.
We will continue to publish new modules and functionality. To be informed when new capabilities are added, check this page or sign up for our Twitter feed.
How to Use the RNA-seq Suite
The GenePattern team is developing the RNA-seq suite for the Broad public server. To use the suite now, we recommend that you run these modules on a local GenePattern server, which you can install by doing the following:
- If you have not downloaded GenePattern and installed it on your local machine, instructions for installing a local GenePattern server are
provided on the Download GenePattern page.
- If you have already downloaded and installed a GenePattern server,
follow the instructions for installing suites from the repository to install the RNA-seq suite. The page will present all available
suites. You only need to select the RNA-seq suite checkbox.
Alignment
Bowtie.aligner
Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. For more information, please refer to the Bowtie documentation.
Differential Expression
Cufflinks.cuffdiff
Cufflinks.cuffdiff finds significant changes in transcript expression, splicing, and promoter use. For more information, please refer to the Cufflinks documentation.
Genome Annotation
Cufflinks
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-seq samples. It accepts aligned RNA-seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. For more information, please refer to the Cufflinks documentation.
Cufflinks.cuffcompare
Cufflinks.cuffcompare helps analyze the transcribed fragments (transfrags) in an assembly by comparing assembled transcripts to a reference annotation and tracking Cufflinks transcripts across multiple experiments (e.g., across a time course). For more information, please refer to the Cufflinks documentation.
Scripture
Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. Scripture has been implemented in GenePattern as a pipeline containing several of the functions wrapped as individual modules. Please note: that the modules must be executed as part of the Scripture pipeline. For more information, please refer to the Scripture documentation.
Isoform Detection
TopHat
TopHat aligns RNA-seq reads to a genome in order to identify exon-exon splice junctions. It is built on the ultrafast short read mapping program Bowtie. For more information, please refer to the TopHat documentation.
RNA Quantitation
Cufflinks
Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-seq samples. It accepts aligned RNA-seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one. For more information, please refer to the Cufflinks documentation.
Scripture
Scripture is a method for transcriptome reconstruction that relies solely on RNA-Seq reads and an assembled genome to build a transcriptome ab initio. Scripture has been implemented in GenePattern as a pipeline containing several of the functions wrapped as individual modules. Please note: that the modules must be executed as part of the Scripture pipeline. For more information, please refer to the Scripture documentation.
Utilities
Bowtie.indexer
The Bowtie.indexer builds a Bowtie index from a set of DNA sequences. This module takes a file or ZIP archive of files in either FASTA or FASTQ format, and outputs a set of 6 files. These files together constitute the index. For more information, please refer to the Bowtie documentation.
BamToSam
This module converts a BAM file to a SAM file.
ExprToGct
This module converts a file in EXPR format to GCT format. The EXPR file format is a tab-delimited format produced by Cufflinks.
SamToBam
This module converts a SAM file to a BAM file.
SortSam
This module sorts a SAM or BAM file according to a parameter specified by the user and outputs a sorted SAM or BAM file.
Visualizers
IGV
IGV is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations. For more information, please refer to the IGV documentation.
