D. mel gene table with strand and position data? Investigating strand bias

Question

[cmcallester]

I'm hoping to explore strand bias in functional elements in D. melanogaster, starting with protein coding genes. However, I'm having trouble finding a table-like data set of genes with chromosome, position, and strand listed. Previous literature on strand bias in Drosophila would also help!

[goodez]

One question I have for your study... Are you just considering genes, or also their transcripts?

Because, for example, a single gene on the + strand may have 9 different transcripts. Would you count this as a single gene on the + strand, or 9 copies?

Answer 1

[goodez]

From Ensembl you can download GTF/GFF annotations which have strand information (and much more information). https://useast.ensembl.org/info/data/ftp/index.html

Or simply use BioMart and you can make your own "table-like data set". Let me know if you want more instructions on how to output this table. http://useast.ensembl.org/biomart/martview/62f8efb4cf6a36cb3b31ba61b4a51362