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Old 05-14-2013, 09:17 AM   #1
ssharma
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Location: Georgia

Join Date: Oct 2010
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Default How to align reads to multiple index in bowtie2

Hi,
I am using bowtie2 to align reads to a huge reference data set.
The data set was large so i need to make 3 chunks and index them separately.
Now how to align my reads to those 3 index.

Can i give 3 index one time ?
like -x index1, index2, index3

Thanks
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Old 05-14-2013, 11:59 AM   #2
westerman
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No. As far as I know you can only use one index at a time. You can run bowtie2 three times and should be able to merge the resulting BAM files. On the other hand this multi-index may create multiple mappings that you would not find with a single index.
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Old 07-15-2013, 08:34 PM   #3
Kennels
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Location: Sydney

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Quote:
Originally Posted by ssharma View Post
Hi,
I am using bowtie2 to align reads to a huge reference data set.
The data set was large so i need to make 3 chunks and index them separately.
Now how to align my reads to those 3 index.

Can i give 3 index one time ?
like -x index1, index2, index3

Thanks
Hi ssharma,

I am having the same issue. Did you find a way around your problem? Perhaps by finding a way to index a large reference using bowtie2?
I want to avoid aligning to multiple indexes for the same reference due to the issue westerman pointed out above.
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Old 07-16-2013, 03:13 AM   #4
GenoMax
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Quote:
Originally Posted by Kennels View Post
Hi ssharma,

I am having the same issue. Did you find a way around your problem? Perhaps by finding a way to index a large reference using bowtie2?
I want to avoid aligning to multiple indexes for the same reference due to the issue westerman pointed out above.
Bowtie2-build indexer uses 32-bit pointers internally so there is no way to get around the (under) 4GB size limit.

BWA does allow for genomes over 4 GB (as long as any individual chromosome stays under 2 GB).
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