Difference between revisions of "GenomeTools"
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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, | 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. | which seems futile. For reading the reverse strand, -p is required. | ||
| + | |||
| + | the '''-outfmt''' can be interesting, though maybe not useful. See the help for more details ... multple definitions need only be separated by whitespace. | ||
| + | |||
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 | ||
Latest revision as of 15:49, 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.
the -outfmt can be interesting, though maybe not useful. See the help for more details ... multple definitions need only be separated by whitespace.
This is a Stefan Kurtz contribution, and can be found in the code under
genometools-1.5.9/src/tools/gt_repfind.c
