Question: Found a raw data file; which -omics technology is this output from?
0
gravatar for biohack92
2.4 years ago by
biohack92150
United States
biohack92150 wrote:

I need to identify where this output file was generated from. I would like to analyze it and I'm 99% sure it's RNA seq data, but I need more information on the generated data before I can identify which bioconductor package would be useful. I appreciate any help.

enter image description here

https://drive.google.com/open?id=0B5uoYE0PlQ1rbl9rYWRlQWJYVVU

sequencing rna-seq next-gen • 651 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by biohack92150
1

A google drive link to a file from a stranger on the net ...

Perhaps posting a screenshot would be safer?

ADD REPLYlink written 2.4 years ago by genomax64k
1

My mistake; updated the original post.

ADD REPLYlink written 2.4 years ago by biohack92150

What's to the right of the table? This is mainly just transcript aliases and gene annotation...

ADD REPLYlink written 2.4 years ago by WouterDeCoster37k
1

Any idea where this came from (I guess you don't and perhaps that is the origin of this question)? It looks like some sort of summary of an alignment with counts assigned to intervals/genes. Could be any *-seq (replace * with your favorite method) though since one of the columns is referring to average coverage.

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by genomax64k

I agree, at least this is not raw data. Looks like a biomart export from the mouse genome enriched with read counts, coverage, etc, it mentions only mouse genes, not transcripts. I doubt that this can be further analyzed without the experimental annotation. Indeed, biological data without backing meta-data is pretty much useless.

ADD REPLYlink written 2.4 years ago by Michael Dondrup45k
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