bowtie - ebtw human index

Question

[dentepre]

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 :)

[GenoMax]

Have you checked the premade indexes available here?

[dentepre]

@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.

[ATpoint]

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.

[dentepre]

@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.

[ATpoint]

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.