Posts

Showing posts from September 12, 2010

ngs / high-throughput sequencing pipeline

Image
This is the minimal set of preprocessing steps I run on high-throughput sequencing data (mostly from the Illumina sequencers) and then how I prep and view the alignments. If there's something I should add or consider, please let me know.
I'll put it in the form of a shell script that assumes you've got this software installed.
I'll also assume your data is in the FASTQ format. If it's in illumina's qseq format, you can convert to FastQ with this script by sending a list of qseq files as the command-line arguments.
If your data is in color-space, you can just tell bowtie that's the case, but the FASTX stuff below will not apply.
This post will assume we're aligning genomic reads to a reference genome. I may cover bisulfite treated reads and RNA-Seq later, but the initial filtering and visualization will be the same. I also assume you're on *Nix or Mac.

SetupThe programs and files will be declared as follows.
#programs fastqc=/usr/local/src/fastqc/FastQ…