The folks at EBI have produced a summary of all the high throughput sequence aligners commonly used (link), and there is a companion paper in the current issue of Bioinformatics. The timeline is a fascinating info-graphic.
There is also a table describing the features of each. One thing I noticed is that there are relatively few aligners for RNA data, despite RNA-seq being arguably the most important application in NGS right now. (I will cover the use of RNA specific aligners in future posts.) The paper discusses some of the generalities of selecting an appropriate alignment tool for the job but doesn't go so far as to suggest which one is "best".
In our RNA-seq series so far we've performed differential analysis and generated some pretty graphs, showing thousands of differentially expressed genes after azacitidine treatment. In order to understand the biology underlying the differential gene expression profile, we need to perform pathway analysis.
We use Gene Set Enrichment Analysis (GSEA) because it can detect pathway changes more sensitively and robustly than some methods. A 2013 paper compared a bunch of gene set analyses software with microarrays and is worth a look.
Generate a rank file
The rank file is a list of detected genes and a rank metric score. At the top of the list are genes with the "strongest" up-regulation, at the bottom of the list are the genes with the "strongest" down-regulation and the genes not changing are in the middle. The metric score I like to use is the sign of the fold change multiplied by the inverse of the p-value, although there may be better methods out there (link).
In the last post of this series, I left you with a gene expression profile of the effect of azacitidine on AML3 cells. I decided to use the DESeq output for downstream analysis. If we want to draw a heatmap at this stage, we might struggle because the output provided by the DEB applet does not send back the normalised count data for each sample.
It is not really useful to plot all 5704 genes with FDR adjusted p-values <0.05 on the heatmap, so I will simply show the top 100 by p-value. Here are the general steps I will use in my R script below:
Read the count matrix and DESeq table into R and merge into one tableSort based on p-value with most significant genes on topSelect the columns containing gene name and raw countsScale the data per rowSelect the top 100 genes by significanceGenerate the heatmap with mostly default values
Google searches show that R has some quite elaborate heatmap options, especially with features from ggplot2 and RColorBrewer. In this example, I will use buil…
Aligning reads to the genome is a key step in nearly all NGS data pipelines, the quality of an alignment will dictate the quality of the final results. So for beginners in this space, the options available can be a bit overwhelming.
Which options are available?
Depending on what species you are working on, you will have either a limited number of choices or a vast number of choices. These include NCBI, Ensembl, UCSC as well as the consortia that generate these genome builds, such as the Human Genome Reference Consortium for human and TAIR for Arabidopsis. My recommendation at this point is Ensembl, for a number of reasons: It is clear to see what genome build and version just from the file names. Contrast "hg38.fa.gz" for UCSC vs "Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz" for EnsemblFrom the Ensembl file name you can tell whether its masked, and whether its "primary assembly" or "toplevel".The website is intuitive, ftp downloads are fast…