Genome Annotation

Usage -i mytable -a rmsk.gtf.gz -u -c1,2,3 -n rmsk -o mytable_rmsk



-a      Sorted Annotation file in GTF format

-i      Annotate a file of positions [column1=region, column2=coordinate (1 based)] or a single position [region:coordinate (1 based)]

-s      Strand column in annotation file [4]

-u      Not use table strand info (fix it to 2)

-c      Add columns separated by comma (feature:1, gene_id:2, transcript_id:3) [1,2]

-n      Column name [Col]

-S      Correct strand by annotation

-C      Columns with base distribution [7,12] (in combination with -S)

-o      Save lines to a file

-h      Print the help

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