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Question: how to create index
0
gravatar for Bioinformatics
12 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 

 

rsubread • 234 views
ADD COMMENTlink modified 12 months ago by Mike Smith3.2k • written 12 months ago by Bioinformatics30
Answer: how to create index
0
gravatar for Mike Smith
12 months ago by
Mike Smith3.2k
EMBL Heidelberg / de.NBI
Mike Smith3.2k 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 12 months ago by Mike Smith3.2k
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