Agenda

November 16, 2015 · View on GitHub

Nov 2-3, 2015.

Starting at 9:15am, going until noon, with a coffee break;

1-3pm, individual/group consultation

Using Salmon to quantify RNAseq

Salmon is one of a breed of new, very fast RNAseq counting packages. Like Kallisto and Sailfish, Salmon counts fragments without doing up-front read mapping. Salmon can be used with edgeR and others to do differential expression analysis.
Using Salmon to eliminate low-expressed transcripts

In many assemblies - especially de novo assemblies, done without a reference genome - there are many transcripts that don't have significant expression levels. This can interfere with quantification and annotation. We can use Salmon to eliminate many of these transcripts, by estimating their transcription levels and removing low-expressing transcripts.
Using transrate to evaluate RNAseq assemblies

How do you measure the quality of your transcriptome? In some of the beginner workshops, we suggested mapping your RNAseq reads back to the transcriptome and counting the fraction that mapped. Transrate takes this kind of idea quite a bit further and measures several read-based metrics.
Make and share your reference-based transcriptome

This tutorial shows how to build a new transcriptome with Cufflinks and share it as a custom track on the UCSC Genome Browser, using github to store the files.
Run 'diamond', a faster BLAST-like program

BLAST things faster!
Annotate transcripts with KEGG