Differences between revisions 2 and 3
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| Aligns current set of all SGN unigenes to the genome. Runs GenomeThreader as `gth -xmlout -minalignmentscore 0.90 -mincoverage 0.90 -seedlength 16 -species arabidopsis -cdna sgn_unigenes.fasta -genomic <contig/bac seq>` |
Aligns current set of all SGN unigenes to the genome. Runs GenomeThreader as {{{ 'gth', '-gff3out', '-intermediate', '-force', -autointroncutout => 200, '-gcmaxgapwidth' => 25000, #< max gap in any alignment, this is 1.2x the largest intron size we have seen so far -minalignmentscore => '0.90', -mincoverage => '0.90', -seedlength => 16, -o => "$temp_gff3", -species => 'arabidopsis', -cdna => "$temp_cdna", -genomic => $un_xed_seqs, }}} |
Summary
Tag |
sgn_unigenes |
Owner |
SGN |
Input |
contig or BAC sequences |
Output |
GenomeThreader alignments of SGN unigenes to the genome |
Depends |
seq |
Aligns current set of all SGN unigenes to the genome. Runs GenomeThreader as
'gth',
'-gff3out',
'-intermediate',
'-force',
-autointroncutout => 200,
'-gcmaxgapwidth' => 25000, #< max gap in any alignment, this is 1.2x the largest intron size we have seen so far
-minalignmentscore => '0.90',
-mincoverage => '0.90',
-seedlength => 16,
-o => "$temp_gff3",
-species => 'arabidopsis',
-cdna => "$temp_cdna",
-genomic => $un_xed_seqs,
Input
un-Xed contig/BAC sequence from seq analysis (AnSgnChecks000)
Requirements
- genomic sequences, no X masking, fasta format
Processing
Runs GenomeThreader as gth -xmlout -minalignmentscore 0.90 -mincoverage 0.90 -seedlength 16 -species arabidopsis -cdna sgn_unigenes.fasta -genomic <contig/bac seq>
Output
GenomeThreader XML, GFF3 representation of the GenomeThreader results
Filenames
gth:xml, unigenes:gff3
Requirements
- valid gthxml, valid GFF3