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Question: how to create index
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gravatar for Bioinformatics
6 months ago by
Bioinformatics30 wrote:

how can i use Rsubread​ to make the index based on human reference? i could not find the command 

In their documentation, I can see the following 

ref <- system.file("extdata","reference.fa",package="Rsubread")
buildindex(basename="reference_index",reference=ref)​

but I don't know how to build it based on human 

 

ADD COMMENTlink modified 6 months ago by Mike Smith2.8k • written 6 months ago by Bioinformatics30
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gravatar for Mike Smith
6 months ago by
Mike Smith2.8k
EMBL Heidelberg / de.NBI
Mike Smith2.8k wrote:

In that example ref <- system.file("extdata","reference.fa",package="Rsubread") gives the path to a file.  You can see this simply by printing it out.  For me this is

> ref
[1] "/g/R-devel/library/Rsubread/extdata/reference.fa"

So you need to get a FASTA file for the genome you want to use, and then use the path to that file for ref, so something like ref <- "c:/path/to/hg19.fa" or ref <- "/path/to/hg19.fa" depending on if you're using Windows or not.

You should then be able to use the buildindex() function in the way described.

ADD COMMENTlink written 6 months ago by Mike Smith2.8k
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