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Annotation tracks for pan troglodytes

asked 2015-03-23 13:30:11 -0600

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Dear all,

I would like to open some BAM files from RNAseq data generated from chimpanzee CNS. Unfortunately I could not find annotation track from the Pan troglodytes to download and use within the GenomeBrowse. Are there any annotation files for Chimpanzee that are available for GenomeBrowse that could be downloaded elswere? or is there any other approach to solve this problem?

Kind regads Martin

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answered 2015-12-31 10:02:58 -0600

Hi Martin,

I wanted to let you know that we have been able to add support for the chimp assemblies PanTro3 and PanTro4 to GenomeBrowse.

You can download the reference sequence tracks for both assemblies and the gene annotation source for the PanTro4 assembly by going to Add and selecting them from the Public Annotations location. They are listed under builds CSAC2.1.3 and CSAC2.1.4 for the Pan troglodytes species.

Let me know if you have any issues or further questions.

Thanks, Jami...

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answered 2015-04-27 09:12:02 -0600

Hi Martin,

As follow-up from our email discussion I wanted to see if you were able to successfully add the custom genome for Chimpanzee into GenomeBrowse?

You can curate your own reference sequence by converting the FASTA reference that was used to align your sequences and create your BAM files. To do this go to Add and select Convert in the lower left corner, add your FASTA file and follow the prompts to create the reference sequence.

You can find an example workflow for this process in a tutorial we have for our analytic software SVS at the following link, the process is very similar in GenomeBrowse. Create Custom Genome Assembly

Once the conversion is complete you will want to close and reopen GenomeBrowse for the new source to be available, then select the new genome build from the assembly dropdown and your BAM files should correctly draw in GenomeBrowse.

Alternatively we can also create the reference sequence and have it available from our Public Annotations repository. If you can provide a link to a public source of the references sequence I can add it to our list of genomes to curate.

Let me know how I can help you further.

Thanks, Jami…

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Asked: 2015-03-23 13:30:11 -0600

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Last updated: Dec 31 '15

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