[BioC] Regarding subread vignette

[Wei Shi]

Dear Rashi,

The buildindex function uses all chromosomal files to build a index for a
reference genome, eg. mouse genome. You should run buildindex only once
either with a list of chromosomal file names or with a single file which
is concatenated from all chromosomal files.

To create a single file which includes all the chromosomal sequences, you
can use the following unix command (run it on a unix shell):

cat chr1.fa chr2.fa chr3.fa ... > mm9_all.fa

The concatenation will take several minutes and the index building will
take about 1 hour for mouse genome.


Cheers,
Wei

> Dear Dr. Shi,
>
>    I wanted to use Rsubread vignette for alignment of single read RNA
> sequencing data from GAIIx. As I understand before aligning my reads I
> need
> to build index for reference genome (mouse in my case). Since I'm very new
> to
> this field and this is the first time I'am dealing with sequencing data I
> have some doubts how to do this and your help in this regard is very
> appriciated.
>
>    As mentioned in below example I understand that the extdata is the
> directry for the indexed genome which is created but what is
> "reference.fa".
> Is this the fasta file for single chromosome (which means I have to repeat
> this for all the chromosomes one by one).
>
>>library(Rsubread)
>>ref <- system.file("extdata", "reference.fa", package = "Rsubread")
>>path <- system.file("extdata", package = "Rsubread")
>>buildindex(basename = file.path(path, "reference_index"), reference =
>> ref)
>
> Thanks in advance for your help.
>
> Regards,
> Rashi Halder
>
>



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