Saturday, April 29, 2017

Mira4 assembly of 454 reads from SRA

I want to make an assembly of the Annona squamosa fruit transcriptome data from this paper (http://dx.doi.org/10.1186/s12864-015-1248-3). They give in the paper a link to a web resource (http://www.annonatranscriptome.nabi.res.in/), but the resource appears to now be defunct, so to get contigs reads, I will have to assemble the reads myself. The reads are from two different cultivars of Annona squamosa, so I'm going to assemble each cultivar separately first, and then if that works, I'll try a combined assembly.

MIRA is a nice, free, software package that can assemble 454 data. I've had success with it before, so that's what I'll use for this project too.


Monday, March 20, 2017

Tips for Methods Development and Optimization in Biology



I haven't posted anything in quite a while. Mostly that's because I haven't written anything that I thought would be of general interest. I once again have a young lab assistant to preach at, so I might as well preach at the world too. Here is what I've written for her about methods development in the biology laboratory.