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Question: Orthologus Regions
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8.6 years ago by
research pal • 40
research pal • 40 wrote:
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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modified 8.6 years ago by Guruprasad Ananda • 230 • written 8.6 years ago by research pal • 40
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8.6 years ago by
Guruprasad Ananda • 230
Guruprasad Ananda • 230 wrote:
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.
ADD COMMENT • link written 8.6 years ago by Guruprasad Ananda • 230
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