buildLoci

A utility to build gene loci (i.e., sets of overlapping transcripts) out of a transcript set.

Usage example:

bedtools intersect -s -wao -a inGTF -b inGTF | buildLoci.pl - > test.loci.gff

The input file is provided as first argument to the script. It consists in two ("left" and "right") GTF records per line, separated by a tab. This is typically the standard output produced by bedtools intersect -wao -a inGTF -b inGTF (inGTF being a single GTF file).

The flexibility of bedtools allows the user to build gene loci based on whatever definition they need, e.g., with or without respect to genomic strand (see bedtools's -s option).

• keepGeneid = If set, any gene_id values present in the input will be kept in the output, under attribute gene_id_bkp.
• locPrefix (string) = When set, this parameter's value will be prepended to all gene_id values in the output (in the form of <locPrefix>LOC_XXXXXXXXXX)

One GTF line per unique "left" GTF record in the input, with a supplementary gene_id attribute (in the form of LOC_XXXXXXXXXX) appended to its 9th field.

Any gene_id value present in the input will be overwritten, except if the --keepGeneid option is used.

Any pair of GTF records present within a line of input is assumed to represent overlapping features. Gene loci are then built based on these overlaps, i.e. the <transcript_id>s of both records are assigned the same arbitrary <gene_id> value in the output.

Although not strictly necessary, BEDTools is recommended, solely to provide input to buildLoci.pl.

Julien Lagarde, CRG, Barcelona, contact [email protected]