Changes between Version 37 and Version 38 of SOPs/rna-seq-diff-expressions

Timestamp:

05/05/17 10:16:06 (8 years ago)

Author:

thiruvil

Comment:

--

SOPs/rna-seq-diff-expressions

@@ -172 +172 @@
       * [[http://www.ncbi.nlm.nih.gov/pubmed/21176179|From RNA-seq reads to differential expression results]] - Oshlack A, Robinson MD, Young MD.  Genome Biol. 2010;11(12):220. Epub 2010 Dec 22.
    * For more practical information, see the third session of [http://jura.wi.mit.edu/bio/education/R2011/ An introduction to R and Bioconductor: A BaRC Short Course] and the  [http://jura.wi.mit.edu/bio/hot_topics/ BaRC Hot Topic] (under "Short Read Sequencing", see "Practical RNA-Seq analysis")
+
+== Others: Alignment-free ==
+  *  k-mer indexing/counting: \\
+    *  [[http://www.cs.cmu.edu/~ckingsf/software/sailfish/ | Sailfish ]]: ultrafast isoform abundance estimation from RNA-seq reads
+    *  [[https://combine-lab.github.io/salmon | Salmon ]]: successor of Sailfish
+    *  [[https://pachterlab.github.io/kallisto | Kallisto]]: quantifying abundances of transcripts from RNA-Seq data
+    *  [[http://pachterlab.github.io/sleuth/ | Sleuth]]: assay differential expression after quantification (eg. from Kallisto)