Category: BINF 6215

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...

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...

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...

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...

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...

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...

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...

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...

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...