I would like display the Cambridge Reference Sequence (rCRS) of the Human Mitochondrial DNA in GenomeBrowse. In particular, i aligned some mitochondrial dna sequences with clustalw and then I would like display these alignment results in GenomeBrowse. Someone can help me?
Hi Alberto,
I am happy to help you with your GenomeBrowse Questions.
The Revised Cambridge Reference Sequence (rCRS) of the Human Mitochondrial DNA is contained withing our full GRCh_37_g1k version of the human reference sequence. The track is labeled "Reference Sequence, 1000Genomes" and can be download or streamed through the Annotations Tab of the Add dialog.
To use this reference sequence to visualize your BAM files you will need to make sure the header for your BAM correctly identifies the name and length for the mitochondrial region of this track. For the 1000Genomes reference sequence it is chrMT with a length of 16569. You can see what information is contained in the BAM header by loading the file into GenomeBrowse then clicking on the plot name in the Plot Tree and scrolling down to the bottom of the Console.
If you receive any errors it would be easiest for us to diagnosis what is happening if we could take a look at your BAM file directly. If you would be willing to share your file please email us at genomebrowse@goldenhelix.com and we can arrange for a secure transfer of the information.
Please let me know if you have any further questions.
Thanks, Jami...
Questions should be tagged FeatureRequest for asking about a non-existing feature or proposing a new idea, GeneralInquiry for general questions about GenomeBrowse or directions on how to do something, or RanIntoProblem if you want to report an issue or had difficulty getting to an expected result.
Asked: 2013-11-21 15:25:28 -0600
Seen: 1,580 times
Last updated: Nov 25 '13
