how to make rnt file

[bioinfobeginner]

Hi All,

I have a bacterial RNASeq data and I would like to analyse it using Edge-pro and Rockhopper, but both the application require an rnt file (RNAs file). I would be thankful if anyone could tell me how to generate such file or from where to get it.

Thanks!

[peskador]

Hello,

If you have a sequenced bacteria, you can get all info from ncbi ftp

But if you want to you can create one by your own:

Usually the rnt file looks like this:

Bacteria name - 1..6264404
106 RNAs (number sRNAs)
Location Strand Length PID Gene Synonym Code COG Product
298816..298892 - 77 110645304 - PA0263.1 - - Arg tRNA

All spaced with tab (\t)

When I work with EDGE-Pro looking for sRNAs you can put all sRNAs information in this file (with Location standing for start...end) and in the end the Product = sRNA.

If you have any concern please feel free to ask me anything.