blat 36 (with options)
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
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.