How to align reads to multiple index in bowtie2

ssharma · 05-14-2013, 10:17 AM

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

westerman · 05-14-2013, 12:59 PM

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.

Kennels · 07-15-2013, 09:34 PM

Quote:

Originally Posted by ssharma

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.

GenoMax · 07-16-2013, 04:13 AM

Quote:

Originally Posted by Kennels

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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05-14-2013, 10:17 AM	#1
ssharma Member Location: Georgia Join Date: Oct 2010 Posts: 19	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

05-14-2013, 12:59 PM	#2
westerman Rick Westerman Location: Purdue University, Indiana, USA Join Date: Jun 2008 Posts: 1,104	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.