Category: BINF 6215

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: 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...