Question: How do I make a .rnt file for EDGE-pro. What is it, and can it be made from a .gbk file?
2
gravatar for hr.andreaskjaer
3.4 years ago by
United States
hr.andreaskjaer20 wrote:

Hello,

I am working on a transcriptomics experiment. It is for a bacterial genome, that has no .rnt or .ptt file made for it. EDGE-pro which I'm using, requires both of those files. I realized that I could convert a .gbk file to a .ptt file. 
Is there a tool to create .rnt files (from .gbk maybe?), or some ingenious script to extract the information from a .gbk file.
As I understand, .ptt are protein table files and .rnt is non-coding RNA table files.

Hope you can help!

Andreas

rna-seq sequence alignment • 1.9k views
ADD COMMENTlink modified 23 months ago by Ranjit0 • written 3.4 years ago by hr.andreaskjaer20
0
gravatar for malteherold
3.1 years ago by
malteherold20
malteherold20 wrote:

Hi,

sorry that you had to wait 4 months for an answer..

.rnt files contain RNA features usually rRNA, tRNA

you can write .ptt and .rnt files from a genbank file for example with bioperl:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

and select CDS or RNA features with $feature_object->primary_tag and write entries to the according file.

This might also be helpful: Problem combining ptt, rnt files

However note that you need a .ptt or .rnt file for each replicon e.g. when your bacterial genome consists of multiple contigs or contains plasmids.

I wrote a short script to write .ptt and .rnt files from a gff file but I'm not sure how to upload this here, let me know if I should send it to you.

Best,

Malte

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by malteherold20
0
gravatar for Ranjit
23 months ago by
Ranjit0
Ranjit0 wrote:

check this https://github.com/sgivan/gb2ptt

ADD COMMENTlink written 23 months ago by Ranjit0
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