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


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