I would like to programmatically, in R, obtain gene lengths (excluding introns) of genes of c. elegans given their Wormbase identifier (for example: WBGene00000004). How can I do so?

  • $\begingroup$ Hi @AIM Perhaps do this for the translated proteome, e..g. RNA-seq and multiple by 3? More importantly could submit your code you have written to date? It would be quite easy but you do need to access the data for translated gene, which for worms I dunno $\endgroup$
    – M__
    Jun 20 '20 at 0:05
  • $\begingroup$ @Michael could you elaborate a bit about the approach you're suggesting? I'm coming from a computer science background so my knowledge of biology is a bit limited. Additionally, I haven't written any code yet for this. I tried using a function called getGeneLengthAndGCContent from EDASeq as I explain here (bioinformatics.stackexchange.com/questions/13581/…) , but that oddly enough it doesn't seem to be working $\endgroup$ Jun 20 '20 at 0:20
  • 1
    $\begingroup$ I answered the question at Biostars: biostars.org/p/444909 $\endgroup$
    – ATpoint
    Jun 20 '20 at 18:13

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Browse other questions tagged or ask your own question.