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

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!

genome gene drosophila strand bias
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updated by Ram Ram • written by cmcallester • cmcallester

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?

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written by goodez goodez

1 answer

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

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written by goodez goodez

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