Question: bowtie - ebtw human index
0
gravatar for dentepre
5 weeks ago by
dentepre0
dentepre0 wrote:

Hi,

I need index of human genome, but build by bowtie (version 1) and with .ebtw extension. How can I force bowtie to build "small" index of human genome? According to the manual, there is only option to force building "large" index from smaller genome.

Thanks :)

next-gen • 93 views
ADD COMMENTlink written 5 weeks ago by dentepre0

Have you checked the premade indexes available here?

ADD REPLYlink written 5 weeks ago by genomax69k

@genomax Yes, there is avalialbe ready index to download and it works, but I am not big fan of this kind of solution. To be honest, I am not completly sure if the version of genome which I use is completly the same as use for prebuild indexes.

ADD REPLYlink written 4 weeks ago by dentepre0

Either download one of the premade human indices from the bowtie website genomax linked or use default settings. No need to bother yourself with something as standard as indexing a genome. The defaults will do just fine.

ADD REPLYlink written 5 weeks ago by ATpoint19k

@ATpoint Yes, I've tried to run bowtie using default settings. However, the file with human genome is larger than 4.0GB (the limit for "small" genome in bowtie) and bowtie generate .ebtwl files (for "large" genome). For kind of downstraem analysis, I need to have files with .ebtw extension.

ADD REPLYlink written 4 weeks ago by dentepre0

Gb reads as gigabases not bytes. The human genome is 3.2 billion bases. It is not the file size that matters. You can safely download a premade index. People do that all the time and there is nothing wrong with it unless you manipulated the standard reference genome fasta you downloaded which I strongly discourage.

ADD REPLYlink written 4 weeks ago by ATpoint19k
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