Page tree
Skip to end of metadata
Go to start of metadata

You are viewing an old version of this page. View the current version.

Compare with Current View Page History

« Previous Version 11 Next »

Table of Contents

Overview and Objectives

Once raw sequence files are generated (in FASTQ format) and quality-checked, the next step in most NGS pipelines is mapping to a reference genome. For individual sequences of interest, it is common to use a tool like BLAST to identify genes or species of origin. However, a typical example will have millions of reads, and a reference space that is frequently billions of bases, which BLAST and similar tools are not really designed to handle.

Thus, a large set of computational tools have been developed to quickly, and with sufficient (but NOT absolute) accuracy align each read to its best location, if any, in a reference. Even though many mapping tools exist, a few individual programs have a dominant "market share" of the NGS world. These programs vary widely in their design, inputs, outputs, and applications. In this section, we will primarily focus on two of the most versatile mappers: BWA and Bowtie2, the latter being part of the Tuxedo suite (e.g. Tophat2).

Sample Datasets and Reference Genomes

You have already worked with a paired-end yeast ChIP-seq dataset, which we will continue to use here.  We will also use two additional RNA-seq datasets.  The additional data are located in the path:

/corral-repl/utexas/BioITeam/core_ngs_tools/human_stuff 

So, the following are the data you will need:

File NameDescriptionSample
Sample_Yeast_L005_R1.cat.fastq.gzPaired-end Illumina, First of pair, FASTQYeast ChIP-seq
Sample_Yeast_L005_R2.cat.fastq.gzPaired-end Illumina, Second of pair, FASTQYeast ChIP-seq
human_rnaseq.fastq.gzSingle-end Illumina, FASTQHuman RNA-seq
human_mirnaseq.fastq.gzSingle-end Illumina, FASTQHuman microRNA-seq

Now we need to set up the raw data for processing. Stage these files on Stampede from Corral in the fewest possible commands.

 Hint:
cds
cp /corral-repl/utexas/BioITeam/core_ngs_tools/human_stuff/*rnaseq* .

Do you believe that I gave you files of any reasonable quality?  I wouldn't, so you should check it out.

 Hint:
 

BWA - Yeast ChIP-seq

 

Bowtie2 and Local Alignment - Human microRNA-seq

 

BWA-MEM (and Tophat2) - Human mRNA-seq

 

Future Directions

 

  • No labels