A short sequence on short sequence

Posted by & filed under Tutorial.

A quick tutorial to check out primers on NCBI to see what the product size should be and how specific they are. Old school way is just take the primer with NNNs in the middle and blast. TATTCGTTGGAGACTTTATAACCCTNNNNNNNNNNNNNNNNNNNNNAAGGCTTAGAATTGCAAGGTCTATA You will get an output as such…. Scroll down to the alignments…. And look at the coordinates……. Read more »

RNA-Seq: Tophat via iPlant

Posted by & filed under Workflows.

Goal: Use RNA-seq to compare expression between oysters (n=3) pre and post heat shock. Based on IPlant Collaborative Tutorial https://pods.iplantcollaborative.org/wiki/display/eot/RNA-Seq_tutorial Task 1: Align read data to Crassostrea gigas genome. Tophat is a specialized alignment software for RNA-seq reads that is aware of splice junctions when aligning to a reference assembly. 1) Click Apps from DE… Read more »