compare sequencing reads against UCSC genome builds #if $source.source_select=="database" #blat_wrapper.py 0 $source.dbkey $input_query $output1 $iden $tile_size $one_off #else #blat_wrapper.py 1 $source.input_target $input_query $output1 $iden $tile_size $one_off #end if# ${GALAXY_DATA_INDEX_DIR} Genome Build Your Upload File blat

.. class:: warningmark Using a smaller word size (*Minimal Size of Exact Match*) will increase the computational time. .. class:: warningmark Using a larger mismatch number (*Number of Mismatch in the Word*) will increase the computational time. ----- **What it does** This tool currently uses the **BLAT** alignment program. Your short reads file is searched against a genome build or another uploaded file. ----- **Example** - Input a multiple fasta file:: >seq1 TGGTAATGGTGGTTTTTTTTTTTTTTTTTTATTTTT - Use the default settings: - alignment identity must be higher than or equal to 90%. - minimal size of exact match to trigger an alignment is 11. - allow 0 mismatches in the above exact match size. - Search against ce2 (C. elegans March 2004), partial result:: 25 1 0 0 0 0 0 0 + seq1 36 10 36 chrI 15080483 9704438 9704464 1 26, 10, 9704438, ggttttttttttttttttttattttt, ggtttttttttttttttttttttttt, 27 0 0 0 0 0 1 32 + seq1 36 9 36 chrI 15080483 1302536 1302595 2 21,6, 9,30, 1302536,1302589, tggtttttttttttttttttt,attttt, tggtttttttttttttttttt,attttt, ----- **Parameters** - *Minimal Identity* (**-minIdentity**) : In percent, the minimum sequence identity between the query and target alignment. Default is 90. - *Minimal Size of Exact Match* (**-tileSize**) : The size of a match that will trigger an alignment. Default is 11. Usually between 8 and 12. Must be between 6 and 18. - *Number of Mismatch in the Word* (**-oneOff**) : The number of mismatches allowed in the word (tile size) and still triggers an alignment. Default is 0. ----- **Reference** **BLAT**: Kent, W James, BLAT--the BLAST-like alignment tool. (2002) Genome Research:12(4) 656-664.