[galaxy-dev] question about bam and bai

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[galaxy-dev] question about bam and bai

Davide Cittaro
Just a silly one, 
Are bam indexes (.bai) automagically created when a bam file is imported (either from or into a library)? If not, how can I do it?

d
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Davide Cittaro

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Re: [galaxy-dev] question about bam and bai

Daniel Blankenberg
These indexes are implemented as metadata, so each dataset association (library item, history item) will have one created automatically by the framework for this datatype.


On May 26, 2010, at 10:18 AM, Davide Cittaro wrote:

Just a silly one, 
Are bam indexes (.bai) automagically created when a bam file is imported (either from or into a library)? If not, how can I do it?

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/



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Re: [galaxy-dev] question about bam and bai

Greg Von Kuster
In reply to this post by Davide Cittaro
Hi Davide,

By "imported", do you mean imported from / to a history?  If so, then the Bam file has previously been uploaded, at which time the associated index was created.  Importing in this case just means another pointer to the disk file is created.

Greg

On May 26, 2010, at 10:18 AM, Davide Cittaro wrote:

Just a silly one, 
Are bam indexes (.bai) automagically created when a bam file is imported (either from or into a library)? If not, how can I do it?

d
/*
Davide Cittaro

Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
*/



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Greg Von Kuster
Galaxy Development Team




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Re: [galaxy-dev] question about bam and bai

Greg Von Kuster

On May 26, 2010, at 10:39 AM, Davide Cittaro wrote:


On May 26, 2010, at 4:30 PM, Greg Von Kuster wrote:


So, to summarize:
1- a bai file is created when adding a bam to a dataset into data libraries
2- the same bai is referenced when importing from a data library to a history
3- if I create/modify/update a bam file already in history a bai file is automagically created as metadata of the new one (right?)

Yes


what if something went wrong at step 1 and I don't have bai file? how can I recreate it?

Click the pencil icon in the history item and click "Auto-detect" in the Edit Attributes form to re-generate the metadata.


d


Greg Von Kuster
Galaxy Development Team




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