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Old 06-18-2012, 11:59 AM   #1
Arupsss
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Question BowTie Index Builder

I want to use BowTie. I download it and run the example commands given into it. However, I want to build index for read length 150 bps. This command (/.bowtie-build chromosome1.fa bowtieIndex ) seems gives default index bilder means for 36 bps. Can anybody help me how to build BowTie index for 150 bps.

Last edited by Arupsss; 06-18-2012 at 12:15 PM.
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Old 06-19-2012, 08:54 AM   #2
Richard Finney
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I'm no expert, but ... I think ..

The index built for your genome (or chromosome) should be able to handle varying sized read lengths as input to bowtie when doing alignment. The index is not specific to the read lengths that you are trying to align.

The introduction in the bowtie documentation mentions an example 36bp test file. The build is not made from this test file, it's just test data made from the genome (or chromsome). If you need 150bp test data ... well, that's another problem ... likely requiring a little custom scripting.
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Old 06-19-2012, 09:02 AM   #3
chadn737
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Richard is right, the bowtie index can handle multiple read lengths. It even works when you have a mixed length of reads. However, I would recommend bowtie2 over bowtie, particularly for the longer read lengths.
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Old 06-19-2012, 09:17 AM   #4
GenoMax
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You build the index for the reference genome (and not for a particular type/length of reads).

I think you may be confused by the wording in the first para here (http://bowtie-bio.sourceforge.net/ma...what-is-bowtie). The 36-bp is a historical reference to the original read length for illumina reads (which have since been lengthened to 150 bp or more).

Last edited by GenoMax; 06-19-2012 at 09:19 AM.
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Old 06-26-2012, 08:07 AM   #5
mathew
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Default index for viral genome

I want to run TopHAt of viral genome but to make it compatible I guess I need to generate index could some one guide me how can I generate such index files. Is there any web based tool or it is just only possibly only by programming. The particular genome is not available of tophat/ bowtie web page.

Thanks
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Old 06-26-2012, 08:23 AM   #6
chadn737
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Quote:
Originally Posted by mathew View Post
I want to run TopHAt of viral genome but to make it compatible I guess I need to generate index could some one guide me how can I generate such index files. Is there any web based tool or it is just only possibly only by programming. The particular genome is not available of tophat/ bowtie web page.

Thanks
For Tophat: http://bowtie-bio.sourceforge.net/ma...-build-indexer

For Tophat2: http://bowtie-bio.sourceforge.net/bo...-build-indexer
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