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.
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.