Predict Error

[bshim181]

I inputted candidate ORF text file to narrow down the list of ORFs of interest with the TI Seq data.
I am receiving this error after running predict.

Candidate ORFs input file looks something like this.

I was wondering what might be the underlying cause for the error. Thank you!

[zhpn1024]

The input position need to be the relative position within the transcript length.

[bshim181]

Do you have a script that you would recommend to achieve this?
I was wondering what about 5'UTR (Upstream ORFs) or 3'UTR ORFs (downstream ORFs)? How would you expect those ORFs to be converted to transcript positions?

[zhpn1024]

The full length of transcript includes 5'UTR and 3'UTR. The position 0 is the first base of 5'UTR.
I can add an option to support genome start and end positions like your input file.

[bshim181]

That would be wonderful. do you have an idea of when that could be implemented by?

[zhpn1024]

You can test the code to speed up the process. I have just updated the --igenomepos option in this github. Can you git clone and install the latest version?

[bshim181]

i am giving it a try but facing this error. it seems to throw this error for all candidate ORFs?

[zhpn1024]

What's the genome position of ENSMUST...86843.1, are 484..1276 in this range?

[bshim181]

Sorry! I was running with the wrong candidate ORF file. It works now!

[zhpn1024]

Great!

[bshim181]

Hello, I do see this error appear again with the genome transcript. Could there be an issue if the ORFs start within the intron of the transcript?

[zhpn1024]

Yes, the intron positions are considered not in the transcript. They cannot be mapped to the transcript positions.