blat 36 (with options)

Blat_with_options is an app for Blat, the Blast-Like Alignment Tool. This version allows setting options.

Quick Start

• To use blat 36  (with options), upload your data in fasta format.
• Resources: <http://genome.ucsc.edu/FAQ/FAQblat.html>

Test Data

Input File(s)

Use the

Arabidopsis_thaliana.TAIR10.fa as the database file and

AT3G24310.fa as the query file

Parameters Used in App

There following settings can be used:

       -prot       Synonymous with -t=prot -q=prot
       -noHead     suppress .psl header (so it's just a tab-separated file)
       -trimT      Trim leading poly-T
       -noTrimA    Don't trim trailing poly-A
       -trimHardA  Remove poly-A tail from qSize as well as alignments in
               psl output
       -fastMap    Run for fast DNA/DNA remapping - not allowing introns,
               requiring high %ID
       -fine       For high quality mRNAs look harder for small initial and
               terminal exons.  Not recommended for ESTs
       -extendThroughN - Allows extension of alignment through large blocks of N's

Output File(s)

Expect a tab delimited txt file as output, named output.psl or whatever you changed it to. It is in psl format, which can be converted to SAM format.

Tool Source for App

• http://users.soe.ucsc.edu/~kent/src/blatSrc34.zip