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1.  [HCC-DOCS](index.html)
2.  [HCC-DOCS Home](HCC-DOCS-Home_327685.html)
3.  [HCC Documentation](HCC-Documentation_332651.html)
4.  [Running Applications](Running-Applications_7471153.html)
5.  [Bioinformatics Tools](Bioinformatics-Tools_8193279.html)
6.  [Alignment Tools](Alignment-Tools_8193288.html)

<span id="title-text"> HCC-DOCS : BLAT </span>
==============================================

Created by <span class="author"> Adam Caprez</span>, last modified by
<span class="editor"> Natasha Pavlovikj</span> on Dec 12, 2016

| Name | Version | Resource |
|------|---------|----------|
| blat | 35x1    | Tusker   |

|      |      |       |
|------|------|-------|
| blat | 35x1 | Crane |

<span style="line-height: 1.4285715;">  
</span>

<span style="line-height: 1.4285715;">BLAT is a pairwise alignment tool
similar to BLAST. It is more accurate and about 500 times faster than
the existing tools for mRNA/DNA alignments and it is about 50 times
faster with protein/protein alignments. BLAT accepts short and long
query and database sequences as input files.</span>

The basic usage of BLAT is:

**General BLAT Usage**

``` syntaxhighlighter-pre
blat database query output_alignment.txt [options]
```

where **database** is the name of the database used for the alignment,
**query** is the name of the input file of sequence data in
fasta/nib/2bit format, and **output\_alignment.txt** is the output
alignment file. Additional parameters for BLAT alignment can be found in
the
manual: <a href="http://genome.ucsc.edu/goldenPath/help/blatSpec.html" class="external-link">http://genome.ucsc.edu/goldenPath/help/blatSpec.html</a>,
or by using

**Additional BLAT Options**

``` syntaxhighlighter-pre
[<username>@login.tusker~]$ blat
```

Running BLAT on Tusker with query file **input\_reads.fasta** and
database **db.fa** is shown below:

**blat\_alignment.submit**

\#!/bin/sh  
\#SBATCH --job-name=Blat  
\#SBATCH --nodes=1  
\#SBATCH --ntasks-per-node=1  
\#SBATCH --time=168:00:00  
\#SBATCH --mem=50gb  
\#SBATCH --output=Blat.%J.out  
\#SBATCH --error=Blat.%J.err

 

|                       |
|-----------------------|
| module load blat/35x1 |

blat db.fa input\_reads.fasta output\_alignment.txt

Although BLAT is a single threaded program (**\#SBATCH --nodes=1**,
**\#SBATCH --ntasks-per-node=1**) it is still much faster than the other
alignment tools.

 

**BLAT Output**

BLAT output is a list containing the following information: *the score
of the alignment*, *the region of query sequence that matches the
database sequence*, *the size of the query sequence*, *the level of
identity as a percentage of the alignment* and *the chromosome and
position that the query sequence maps to*.

Attachments:
------------

<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[cb\_blat\_module.xsl](attachments/8193292/8127546.xsl)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[crane\_blat\_version.xsl](attachments/8193292/8127547.xsl)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[crane\_modules.xml](attachments/8193292/8127548.xml)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[tusker\_blat\_version.xsl](attachments/8193292/8127549.xsl)
(application/octet-stream)  
<img src="assets/images/icons/bullet_blue.gif" width="8" height="8" />
[tusker\_modules.xml](attachments/8193292/8127550.xml)
(application/octet-stream)