The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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blat 36 (with options)

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

Quick Start

Test Data

Icon

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> Blat

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