Mercurial > repos > petr-novak > repeat_annotation_pipeline2
diff README.org @ 3:e955b40ad3a4 draft default tip
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| author | petr-novak |
|---|---|
| date | Tue, 12 Oct 2021 07:43:54 +0000 |
| parents | cf3cea0a3039 |
| children |
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--- a/README.org Thu Oct 07 07:29:59 2021 +0000 +++ b/README.org Tue Oct 12 07:43:54 2021 +0000 @@ -4,7 +4,7 @@ ** Extract Repeat Library from RepeatExplorer Archive (=extract_re_contigs.xml=) -This toll will extract library of repeats based on RepeatExplorer2 analysis. Library is available as fasta file. +This toll will extract library of repeats based on RepeatExplorer2 analysis. Library is available as fasta file. Tool also filter out all the contig parts which has read depth and length below threshold. Parts of contigs with read depth below threshold are hardmasker. Contigs with full hardmasking are removed completelly ** Format repeat library (=format_repeat_library.xml=) @@ -18,8 +18,9 @@ ** Repeat Annotation (=repeat_annotate_custom.xml=) - Internally annotation is performed using RepeatMasker search. Output from RepeatMasker is parsed to remove duplicated and overlaping annotations, Conflicts in annotations are resolved using hierarchical classification of repeats provided in custom database - + Internally annotation is performed using RepeatMasker search. Output from RepeatMasker is parsed to remove duplicated and overlaping annotations, Conflicts in annotations are resolved using hierarchical classification of repeats provided in custom database. +** TODO Summarize Annotation +This tool will create summary table from GFF annotation. * test data - ~test_assembly_1.fasta~ with ~test_db_1_satellites.fasta~ (include CLASS followed by double underscore - syntax 1)