The best way to obtain chimp regions orthologous to your human
intervals is to fetch human-chimp alignments and convert the same to
intervals. Here's how this can be done:
1. Use "Fetch alignments > Extract pairwise MAF blocks" tool to
extract human-chimp alignments corresponding to your human intervals.
Before using this tool, please make sure that your input file is of
interval/bed format and the build is set to human (hg18/hg19). You can
click the pencil icon next to your dataset name to modify these fields
2. Use "Convert formats > MAF to Interval" tool (and select chimp
under additional species) to convert the output of step 1 to
intervals. This tool will return two files - one with human intervals
that could be aligned with chimp and the other with orthologous chimp
Hope this answers your question.
Thanks for using Galaxy,