RNA Seq References

Trimming

trim_galore
There is no manuscript for trim_galore. When the authors were contacted, they requested that their website be referenced when using program.

Illumina Adapter Sequences
This links to the actual adapter sequences that should be trimmed.

Alignment

Tophat2 Reference
Tophat2 Download
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. Genome Biol. 2013 Apr 25;14(4):R36. PMID: 23618408

Transcriptome Reconstruction

Cufflinks Reference
Cufflinks Download
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Nat Biotechnol. 2010 May;28(5):511-5. doi: 10.1038/nbt.1621. Epub 2010 May 2. PMID:20436464

Quantification

RSEM Reference
sailfish Reference

Differential Expression

voom Reference
DESeq Reference

Protocol Manuscripts

R and Bioconductor for differential expression
Tuxedo Suite