Empty result in first step (Preparing candidate ORFs)

[SuiyueWestlake]

Hi,

• ribotricer version:
• Python version:
• Operating System:

Description

I'm trying to get the short ORFs of whole human genome. So I downloaded the gtf file from Ensembl database. And also the fasta file of cDNA and ncRNA sequence. It is reported some warnings like"Chromosome GL000220.1 does not appear in the fasta". And finally I got an empty result file.

What I Did

ribotricer prepare-orfs --gtf Homo_sapiens.GRCh38.110.gtf --fasta Homo_sapiens.GRCh38.ncrna.fa --prefix ncrna_small_peptide --start_codons ATG,CTG,GTG,TTG

Output

Thank you so much for you help!

Best, Yue

[saketkc]

You need to pass the genome fasta, not the cdna.

[SuiyueWestlake]

Thank you so much for your reply.

In my project, I'm trying to detect some unusual ORFs that may potentially can be translated to peptides. So I think this kind of sequence may exist in cDNA or ncRNA region. This is the reason why I submit the cDNA fasta file. If I submit genome fasta, will I still be able to identify the above ORFs?

[saketkc]

Yes.

[SuiyueWestlake]

Thank you! I will try it now!