Hello Amit,
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 if necessary. 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 intervals.
Hope this answers your question. Thanks for using Galaxy, Guru.
On Apr 30, 2010, at 5:17 AM, research pal wrote:
From: research pal workinformatics@yahoo.com
Hi, I have a bed file for the chimp genome and I want to download the same region for the human genome. Do you have a tool in Galaxy which can help me for these orthologus regions.
warm regards, Amit.
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