[ensembl-dev] next gen sequencing mapping data

[Xose M Fernandez]

Hi Hardip

It may also be worth for you to know that the European Nucleotide 
Archive now supports streamed access over HTTP. So submitting yoru NGS 
data to the SRA archive comes with the added value that you would ve 
able to browse that data from Ensembl, as you can point to these BAMs 
('Manage Your Data' | 'Attach BAM file') and stream slices to visualise 
your reads (ie. to view a small set of aligned reads from within the 
file without having to download an entire BAM).

I hope this helps,
Xose


On 18/03/2011 06:13, Hardip Patel wrote:
> Hi All
>
> I was wondering if anybody has tried or has opinions about using mysql
> tables of Ensembl to store next gen sequencing mapping data. Our lab
> works on variety of projects (small RNA, transcriptome, methylation,
> genome resequencing) in human and mouse.
>
> I was interested in putting all our mapping data coming from different
> projects in one place organized according to the respective genomes.
>
> Main reasons being we can interrogate our data in terms of Ensembl
> annotations of the genomes and compare various data from these two
> species using one co-ordinate system.
>
> For example, if I have miRNA sequencing data from human and mouse. Then
> I would like to see if the transcripts present in human are also present
> in mouse in my dataset for corresponding genomic locations, using
> genomic alignments as the basis for such comparisons and draw meaningful
> information out of it.
>
> I would also appreciate if somebody can point me in the right direction
> in terms of what tables need to be updated, and how to go about it.
>
> Kind regards
>
> --
> Hardip R. Patel
> Bioinformatician, Molecular Genetics Division,
> Victor Chang Cardiac Research Institute,
> Darlinghurst, NSW – 2010, Australia
> (W): +61 – 2 – 9295 8611
> (M): 0449 180 715
>
>
>
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