...
| Table of Contents | ||
|---|---|---|
|
Catch up
To avoid further issues with job submission, let's just copy alignment results to our $SCRATCH area.
| Code Block | ||||
|---|---|---|---|---|
| ||||
mkdir -p $SCRATCH/core_ngs/results
cd $SCRATCH/core_ngs/results
cp /corral-repl/utexas/BioITeam/core_ngs_tools/results/*.* . |
Overview and Objectives
After raw sequence files are generated (in FASTQ format), quality-checked, and pre-processed in some way, the next step in most NGS pipelines is mapping to a reference genome. For individual sequences, it is common to use a tool like BLAST to identify genes or species of origin. However, a normal NGS dataset will have tens to hundreds of millions of sequences, which BLAST and similar tools are not designed to handle.
...
You have already worked with a paired-end yeast ChIP-seq dataset, which we will continue to use here. The paired end data should already be located at For the sake of uniformity, however, we will set up a scratch area and copy over all our sequencing data. To set up our area, execute something like:
| Code Block | ||||
|---|---|---|---|---|
| ||||
$WORK/archive/original/2014_05.core_ngs$SCRATCH/alignment |
We will also use two additional RNA-seq datasets, which are located at:
...