@@ -275,14 +275,18 @@ Annotations in [BED](http://genome.ucsc.edu/FAQ/FAQformat.html#format1), ie tab-
SequenceName StartPosition LastPosition+1
-can be lifted over between genomes using `halLiftover`. halLiftover does a base-by-base mapping between any two sequences in the alignment (following paralogy relations as well).
+can be lifted over between genomes using `halLiftover`. halLiftover does a base-by-base mapping between any two sequences in the alignment (following paralogy relations as well). The output is written in BED (default) or PSL format.
halLiftover mammals.hal human human_annotation.bed dog dog_annotation.bed
will map all annotations in human_annotation.bed, which must refer to sequences in the human genome, to their corresponding locations in dog (if they exist), outputting the resulting annotations in dog_annotation.bed
halLiftover attempts to autodetect the BED version of the input. This can be overried with the `--inVedVersion` option. Columns that are not described in the official BED specs can be optionally mapped as-is using the `--keepExtra` option.
+By default, halLiftover uses spaces and/or tabs to separate columns. To use only tabs (ie to allow spaces within names), use the `--tab` option.
+Annotations in [Wiggle](http://genome.ucsc.edu/goldenPath/help/wiggle.html) format can likewise be mapped using `halWiggleLiftover`
The number of distinct genomes different bases of a set of target genomes align to can be computed using the `halAlignability` tool. The output is in `.wig` format.