[BioC] Elephant shark genome

[Martin Morgan]

On 04/23/2014 03:06 AM, Miguel [guest] wrote:
>
> Is there going to be the elephant shark (Callorhinchus milii) genome, a model cartilaginous fish, stored in Biostrings objects, like other model genomes.
>

Hi Miguel -- not sure what your use case is, can you provide some context?

If you're just looking for fast access to the sequence data using Bioconductor 
tools you could

   1. download the fasta files, maybe (are these what you're looking for??)

wget 
ftp://ftp.ncbi.nlm.nih.gov/genbank/genomes/Eukaryotes/vertebrates_other/Callorhinchus_milii/Callorhinchus_milii-6.1.3/Primary_Assembly/unplaced_scaffolds/FASTA/unplaced.scaf.fa.gz

    2. In R, re-compress and index the file

        library(Rsamtools)
        fa = razip("unplaced.scaf.fa.gz")
        indexFa(fa)

     3. Use, e.g.,

 > fafile = FaFile("unplaced.scaf.fa.rz")
 > seqinfo(fafile)
Seqinfo of length 21203
seqnames                        seqlengths isCircular genome
gi|564982704|gb|KI635855.1|       18507834       <NA>   <NA>
gi|564982701|gb|KI635856.1|       17031706       <NA>   <NA>
gi|564982698|gb|KI635857.1|       16461339       <NA>   <NA>
gi|564982691|gb|KI635858.1|       16433419       <NA>   <NA>
gi|564982688|gb|KI635859.1|       15003573       <NA>   <NA>
...                                    ...        ...    ...
gi|564405817|gb|AAVX02067416.1|        247       <NA>   <NA>
gi|564405816|gb|AAVX02067417.1|        234       <NA>   <NA>
gi|564405815|gb|AAVX02067418.1|        218       <NA>   <NA>
gi|564405814|gb|AAVX02067419.1|        173       <NA>   <NA>
gi|564405813|gb|AAVX02067420.1|         66       <NA>   <NA>
 > idx = c("gi|564982701|gb|KI635856.1|", "gi|564982688|gb|KI635859.1|")
 > which = as(seqinfo(fafile)[idx], "GRanges")
 > getSeq(fafile, which)
   A DNAStringSet instance of length 2
        width seq                                            names
[1] 17031706 TATAACTGGAGTGTATGTATAC...TGTACCGCCCGGGGTGGTGCG gi|564982701|gb|K...
[2] 15003573 AGAGAGAGATAGAGAGAGACAG...TTGATCATGTCAACCCCCCCA gi|564982688|gb|K...

There is also the vignette on creating a BSgenome package

http://bioconductor.org/packages/release/bioc/vignettes/BSgenome/inst/doc/BSgenomeForge.pdf

Martin

> Thank you
>
>   -- output of sessionInfo():
>
> R version 2.14.1 (2011-12-22)
> Platform: i686-pc-linux-gnu (32-bit)
>
> locale:
>   [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8
>   [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8
>   [7] LC_PAPER=C                 LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> --
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