About ORF nucleotide sequence

[lbwfff]

Hi, Sir Thanks for providing excellent tools, but there is a problem that has been bothering me. The ORF information contained in the results of ribotricer includes the start and end positions of the ORF on the chromosome (if I understand it correctly). The value obtained by subtracting the starting position from the ending position is much larger than the ORF length, I guess it is because the length of the intron is subtracted. I want to get the ORF nucleotide sequence information from the result file generated by ribotricer, but I find it very difficult for me. I imagined creating a bed file and then using getfasta to get the sequence, but this did not remove introns for me. Sir, can you recommend a suitable tool or function that can help me get a specific ORF sequence? Thanks, LeeLee

[saketkc]

Thanks for your question? To obtain nucleotide sequence associated with ORFs in ribotricer index, you can use the orfs-seq command:

ribotricer orfs-seq --ribotricer_index <path_to_ribotricer_index> --fasta <fasta>

You can run ribotricer orfs-seq --help to see other options.

Hope this helps, feel free to reopen with any follow up questions.