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Old 05-22-2010, 04:04 PM   #1
Wei-HD
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Default Bowtie Index Question

Dear all,

I have a short question about bowtie index:

What is the difference between these two mouse index:

M. musculus, UCSC mm9 and M. musculus, NCBI v37

Sorry for this, but just have no clue the difference between them.

Many thanks!
Wei
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Old 05-22-2010, 05:00 PM   #2
Ben Langmead
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Hi Wei,

They contain the same sequences, but use different sequence names. mm9 uses the UCSC naming scheme, with names like "chr1", "chr2", etc. NCBI v37 uses the NCBI naming scheme, with names like "gi|149288852|ref|NC_000067.5|NC_000067", "gi|149288852|ref|NC_000067.5|NC_000068", etc.

Thanks,
Ben
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Old 05-23-2010, 01:01 AM   #3
Wei-HD
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Hi Ben,

Thanks a lot for your reply and explanation!

They were built from the same assembly: NCBI m37 mouse assembly (April 2007, strain C57BL/6J) (which is also called UCSC version mm9), right?

And another question is these two prebuilt index were built from which version chromosome sequence Mus_musculus.NCBIM37.56 or Mus_musculus.NCBIM37.57 (according to Ensemble)? Because I have run Tophat with mm9 prebuilt index, and then I need each chromosome sequence to run other downstream program. But on Ensemble, the chromosome version has been updated from Mus_musculus.NCBIM37.56 to Mus_musculus.NCBIM37.57. In order to keep consistent with mm9 index, which version chromosome I should use?

Thank you Ben!

Wei
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Old 05-23-2010, 05:21 AM   #4
Ben Langmead
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Quote:
Originally Posted by Wei-HD View Post
They were built from the same assembly: NCBI m37 mouse assembly (April 2007, strain C57BL/6J) (which is also called UCSC version mm9), right?
Right.


Quote:
Originally Posted by Wei-HD View Post
And another question is these two prebuilt index were built from which version chromosome sequence Mus_musculus.NCBIM37.56 or Mus_musculus.NCBIM37.57 (according to Ensemble)? Because I have run Tophat with mm9 prebuilt index, and then I need each chromosome sequence to run other downstream program. But on Ensemble, the chromosome version has been updated from Mus_musculus.NCBIM37.56 to Mus_musculus.NCBIM37.57. In order to keep consistent with mm9 index, which version chromosome I should use?
According to those filenames, they should both be compatible with NBCI37/mm9 (that's what the "NCBIM37" part denotes). In fact, Ensembl versions going back to 47 seem to be compatible with NBCI37; you have to go back to 46 before it changes to NCBI36.

Thanks,
Ben
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Old 05-23-2010, 07:30 AM   #5
Wei-HD
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Thank you very much Ben!

Best,
Wei
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Old 07-29-2010, 08:15 AM   #6
Ms@New
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Hi,

I have a question about bowtie index, I though this is the right forum to post it.

What exactly bowtie indexes?
I've read :

BWT (same size as T)
Checkpoints (~15% size of T)
SA sample (~50% size of T)

I understand the BWT and Checkpoints, but what is SA sample?

Thanks

--- problem solved, thanks

Last edited by Ms@New; 08-03-2010 at 11:24 AM.
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