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
| Info |
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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 E. coli K12 genome from http://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=fasta&log$=seqview&format=text
and the homoserine kinase gene sequence from http://www.ncbi.nlm.nih.gov/nuccore/NC_010473.1?report=fasta&log$=seqview&format=text&from=2801&to=3733 as test data. Use Import from URL to get the data into your Discovery Environment account.
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:
...
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.