getting reference genome accession number

Question

[fi1d18]

Hey guys,

When I download an RNA-seq experiment from GEO datasets, often I can't find any track of used reference genome accession number from related paper then if I want align the reads from that experiment, from where I can know about reference genome to align against?

[John]

Hello Sarah,

Could you post a link to an example GEO dataset that you are interested in? From there we can either tell you if the Reference genome was specified, or, even better, how to get the Ref. genome yourself from this sort of data (next time) :)

[fi1d18]

Thank you

For example GSE67083, I am always going through the paper but I cant find the reference genome

:(

[John]

OK so on the page for that bit of data (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE67083) theres a link to a file called the Series Matrix Files. In that file, (ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE67nnn/GSE67083/matrix/GSE67083_series_matrix.txt.gz) is a bunch of information relating to how the data was made, including the genome they mapped the maize RNA too.

In future Sarah, try to be as specific as possible when asking questions. Biologists are extremely welcome here, but unlike biological questions, the devil is really in the detail when it comes to bioinformatic questions :)

[fi1d18]

Thank you