Why do my predicted orf have so many stop codons inside

[hawkwoodpps]

Hello,

Why do my predicted orf have so many stop codons inside?
I use following workflow:
1、get thaliana ribo-seq data
2、map to reference genomes
3、filtering data length（for example, choose reads of 28nt）
4、use ribotish to predict (codes like the following)
do ribotish quality -b $i.bam -g xxxxxxxxx.gtf; done
do ribotish predict -b $i.bam -g xxxxxxxxx.gtf -f xxxxxxxxx.fa --longest -o $i.ribotish.txt; done
5、pick the orf's genome position
6、translate the orf reads to piptide fragment

Finalliy，we find many “*“ in the piptide fragment,which mean stop condons.
Why do the results perform like this?

Thank you.

[hawkwoodpps]

I'm very interested in your project,do you have weixin/wechat?

[zhpn1024]

Hello, how do you translate ORF? The options of '--seq' and '--aaseq' in 'ribotish predict' can output the sequences. My weixin is zhpn1024. At 2024-11-13 20:24:02, "syh" ***@***.***> wrote: Hello, Why do my predicted orf have so many stop codons inside? I use following workflow: 1、get thaliana ribo-seq data 2、map to reference genomes 3、filtering data length（for example, choose reads of 28nt） 4、use ribotish to predict (codes like the following) do ribotish quality -b $i.bam -g xxxxxxxxx.gtf; done do ribotish predict -b $i.bam -g xxxxxxxxx.gtf -f xxxxxxxxx.fa --longest -o $i.ribotish.txt; done 5、pick the orf's genome position 6、translate the orf reads to piptide fragment Finalliy，we find many “*“ in the piptide fragment,which mean stop condons. Why do the results perform like this? Thank you. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>