Category: genomics

BINF 2111: Assembly at the Command Line (Lab)

BINF 2111: Assembly at the Command Line (Lab)

Today’s lab task is preparation for developing a script that will assemble a batch of small genome sequence data sets. In our script development process there are four main steps: Figure out the pipeline...

Sidebar: DE with Tuxedo pipeline #usegalaxy

Sidebar: DE with Tuxedo pipeline #usegalaxy

To get around the problems with the software installs in the lab (and that some of you are having installing corset on your own) here is another way to get a full DE gene...

Under the hood: V. vulnificus JY1305

Under the hood: V. vulnificus JY1305

In this case study, I attempted to improve on the draft assembly of a bacterial genome by combining the original and new data, and using new bioinformatics tools that have become available since we first assembled the genome and...

Getting your 23 and Me data into Galaxy

Getting your 23 and Me data into Galaxy

I just happen to have a file with 960,628 lines of personal SNP data from 23 and Me burning a hole in my hard drive. I’m one of the lucky people who gets 23...

Getting your Galaxy to point to a working executable

Getting your Galaxy to point to a working executable

I’m running my own Galaxy and I want to use it to run the SPAdes assembler as part of a Galaxy pipeline, instead of running SPAdes at my command line with shell scripts. Ostensibly, this...

BINF 6215: Trinity and Corset at the command line

BINF 6215: Trinity and Corset at the command line

This tutorial is my version of the workflow for analysis of the Synechocystis PCC6803 gene expression data using Trinity and Corset. Disclaimer: walking through the workflow shows that there is plenty to be skeptical about in...

BINF 6215: Basic variant calling in Galaxy

BINF 6215: Basic variant calling in Galaxy

Remember the chloroplast variant calling tutorial? Turns out, you can implement the same thing in Galaxy. (Sort of). Since the chloroplast files are very small, I’m recommending you do this on Galaxy Main, because...

BINF 6215: command line variant calling

BINF 6215: command line variant calling

Define the problem Ion Torrent sequence for 12 tomato varietal chloroplasts One reference genome (NC_007898) Map the reads to the reference Identify variants specific to each strain Identify the tools Obviously you’ve done some...

Galaxy NGS 101: Synechocystis remix

Galaxy NGS 101: Synechocystis remix

I made a previous version of this tutorial with some actual expression data from our lab. This version uses an already-normalized set of single-end transcriptome data from Synechocystis PCC 6803. (Normalized data here). Trimming and...

BINF 6215: Using bpipe

BINF 6215: Using bpipe

bpipe is part of a relatively recent trend to build pipeline manager tools that work at the command line. Other examples of this trend are Snakemake, Leaf and nestly.  You may want to consider using...