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RNAseq/Transcriptome analysis
- Gene quantification from BAM/BED file reads
- featureCounts (part of the Subread package) – http
- The Tuxedo pipeline: RNAseq with tophat/cufflinks
- one of the first tool suites for transcriptome-aware RNA-seq alignment and quantification
- RNAseq analysis protocol article in Nature Protocols
- TopHat - http://ccb.jhu.edu/software/tophat/index.shtml
- exon-aware sequence alignment (uses bowtie2/bowtie )
- resource bundles for selected organisms (GFF annotations, pre-built bowtie2 references, etc.)
- cuffquant, cuffnorm, cufflinks – http://cole-trapnell-lab.github.io/cufflinks/manual/
- transcript quantification, normalization, differential expression
- HISAT2, StringTie, BallGown suite – https://ccb.jhu.edu/software/hisat2/index.shtml
- from the Johns Hopkins group who brought you the Tuxedo pipeline – but much faster!
- paper: http://www.nature.com/nprot/journal/v11/n9/full/nprot.2016.095.html
- General RNA-seq analysis workflow from Bioconductor:
- DESeq2 – R Bioconductor package
- DESeq (version 1) documentation:
- https://bioconductor.org/packages/release/bioc/vignettes/DESeq/inst/doc/DESeq.pdf
- while DESeq2 is more sophisticated, reading the original documentation is a better introduction to concepts
- DESeq2 documentation:
- kallisto – https://pachterlab.github.io/kallisto/
- RNA-seq pseudoaligner that goes straight from FASTQ to estimated transcript abundances
- blindingly fast – but only to transcriptome
- companion quantification tool is sleuth – http://pachterlab.github.io/sleuth/about
- overview presentation – 2015-10-21-Kallisto.Anna.pdf
- RNA-seq pseudoaligner that goes straight from FASTQ to estimated transcript abundances
- Dhivya Arasappan's Introduction to RNA Seq CCBB summer school course
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