HTtools maps and quantifies retrotransposon integrations. Sequence reads matching the end of the retrotransposon LTR are trimmed of the LTR end and screened against sequences indicating non integration-specific fragments (PBS sequence, LTR-circle, donor plasmid, retrotransposon internal sequences and restriction enzyme recognition site). Reads are then mapped to genome and sorted according to uniquely mapped, mapping to multiple positions and mapping to homologous recombination sites. Uniquely mapped reads are positionned relative to ORF.
Documentation can be found at http://NICHD-BSPC.github.io/httools.
HTtools v1.1