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Problem loading alignment of mitochondrion chromosome

asked 2013-03-06 10:30:31 -0600

Ge Zhang gravatar image

The GenomeBrowse is a great tool to view BAM alignment. But I have problem to view the alignment of mitochrondrion chromosome probably due to the different abbreviation for the mitochondrion chromosome (M vs MT).

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answered 2013-03-07 05:14:58 -0600

Philip Ebert gravatar image

Are you using the 1000 genomes build of GR37? There is another post about 5 questions down from this one in the list labelled "HG19 genome" that references the mitochondrial genome in the 1000 genomes version. We are using that build and have no problems with visualizing the mitochondrial region of the BAM file (Samtools output shows chrM as chromosome for our files, if that is helpful)

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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: 2013-03-06 10:30:31 -0600

Seen: 398 times

Last updated: Mar 07 '13