Category: BINF 6215

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...

BINF 6215: command line challenge project

BINF 6215: command line challenge project

Now that you’ve worked at figuring out some command line software and made a basic bash script, we’re going to work on a better bash script.  Your challenge (which may stretch over today and...

BINF 6215: Building a bash shell script

BINF 6215: Building a bash shell script

At this point you should have a series of command lines that you have vetted by manually testing the complete workflow on one of your chloroplast sequences.  Here’s my solution — I used the FASTX...

BINF 6215: Figuring out UNIX command line software

BINF 6215: Figuring out UNIX command line software

The most common things that you’ll want to do with shell scripts in bioinformatics are 1) data manipulation (which is what we practiced this morning) and 2) driving programs to run automatically, collecting their...

BINF 6215: Galaxy NGS 101

BINF 6215: Galaxy NGS 101

This tutorial draws on some of the online Galaxy tutorials (here) and videos (here) but I have made some of the steps more explicit for you with screenshots. Galaxy data formats You can think...

BINF 6215: Shell scripting 101

BINF 6215: Shell scripting 101

Shell scripting is a powerful way to string commands together, make commands repeat themselves on a list of files, and all manner of other useful conglomerations of function. Scripting isn’t really “programming” per se...