Difference between revisions of "GenomeTools"
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== Repfind == | == Repfind == | ||
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| + | the '''gt suffixerator''' program has to be run first, to create necessary indeices and other useful files | ||
| + | |||
| + | gt suffixerator -db Repfind-example.fna -indexname repidx2 -v -dna -suf -tis -lcp -ssp -pl | ||
| + | |||
| + | Note how the mnemonics are not great, particularly db meaning input file. Then we can try | ||
| + | |||
| + | gt repfind -f -r -l 4 -ii repidx2 | ||
| + | |||
| + | Despite the -r may be meaning reverse, as in reverse strand here, it is not. It actually refers to the same strand, but in the reverse reading direction, | ||
| + | which seems futile. For reading the reverse strand, -p is required. | ||
This is a Stefan Kurtz contribution, and can be found in the code under | This is a Stefan Kurtz contribution, and can be found in the code under | ||
genometools-1.5.9/src/tools/gt_repfind.c | genometools-1.5.9/src/tools/gt_repfind.c | ||
Revision as of 12:31, 9 October 2017
Introduction
Typically use in conjunction with bedtools and bedops.
Includes AnnotationSketch, which is able to render a PNG image from a gff file.
Its commands start with a gt and then a subcommand, such as gff3validator or sketch.
Tools
Repfind
the gt suffixerator program has to be run first, to create necessary indeices and other useful files
gt suffixerator -db Repfind-example.fna -indexname repidx2 -v -dna -suf -tis -lcp -ssp -pl
Note how the mnemonics are not great, particularly db meaning input file. Then we can try
gt repfind -f -r -l 4 -ii repidx2
Despite the -r may be meaning reverse, as in reverse strand here, it is not. It actually refers to the same strand, but in the reverse reading direction, which seems futile. For reading the reverse strand, -p is required.
This is a Stefan Kurtz contribution, and can be found in the code under
genometools-1.5.9/src/tools/gt_repfind.c
