pipemg / rnaseq_workflow Goto Github PK

This repository will eventually contain the standardized analysis protocol used in the Resendis lab. At the moment this is still in planning and benchmarking phase.

• IGV -> https://www.broadinstitute.org/igv/
• FastQC -> www.bioinformatics.babraham.ac.uk/projects/fastqc/

• STAR -> https://github.com/alexdobin/STAR
• kallisto -> https://pachterlab.github.io/kallisto/
• TopHat -> https://ccb.jhu.edu/software/tophat/index.shtml
• salmon -> http://combine-lab.github.io/salmon/
• HTSeq -> http://www-huber.embl.de/HTSeq/
• RSubread -> https://bioconductor.org/packages/release/bioc/html/Rsubread.html
• StringTie -> http://www.nature.com/nbt/journal/v33/n3/full/nbt.3122.html
• RSEM -> https://github.com/deweylab/RSEM/ (used by TCGA)

• DeSeq2 -> https://bioconductor.org/packages/release/bioc/html/DESeq2.html
• edgeR -> https://www.bioconductor.org/packages/3.3/bioc/html/edgeR.html
• sleuth (for kallisto and salmon) -> https://pachterlab.github.io/sleuth
• limma + voom -> https://www.bioconductor.org/packages/release/bioc/html/limma.html

• DE gene calling -> http://www.genomebiology.com/2013/14/9/R95 limma voom wins, edgeR and DeSeq also good, cuffdiff very high FPR
• DE Gene calling (high replicates) -> http://arxiv.org/pdf/1505.02017v2.pdf edgeR, DeSeq and limma the best but very conservative
• Counting -> http://arxiv.org/pdf/1505.02710.pdf (kallisto paper) kallisto best, RSEM 2nd, Tophat + Cufflinks worst
• Isoform quantification -> http://mikelove.github.io/eurobioc2015 In accuracy alpine (not readu yet) best, kallisto and RSEM 2nd, cufflinks the worst

• Bowtie2 + Tophat2 + Cufflinks
• STAR + RSEM
• STAR/Tophat2 + HTSeq
• Kallisto
• Salmon