Bohoon Shim

This is the ORF annotation file for ribotricer. I was wondering what the coordinates of the last column stand for. This is the ORF annotation for the same transcript_ID by...

Hello, I have been working to transform the Ribotricer index to the RibORF index. I have noticed that the exon boundaries coordinates are not multiple of 3 while RibORF index...

I tried running ribotish quality with the same custom gtf and it returned 0 counted reads. for file in "input_dir"/*; do file_name=$(basename "$file" .fastq) STAR --runThreadN 16 \ --genomeDir custom_gtf_index...

quality figures look good with the known protein coding annotation input. I am wondering why the error still persists in predict step.

based on the message in the beginning, it seems like the para files generated from ribotish quality was read in as an input. It still throws this error, however.

I am currently running singular bam files just as a test. Still getting that error. ribotish predict -b ${out_dir}/STAR_output_TE_Onlys/MC38VehCHX_S1_R1_001_ATCGTAligned.sortedByCoord.out.bam -t ${out_dir}/STAR_output_TE_Onlys/MC38vehLTM_S3_R1_001_ATCGTAligned.sortedByCoord.out.bam -f $reference_assembly -g custom_gtf -o ${out_dir}/ribotish/Test_TE_Transcripts.txt -v --aaseq --inframecount...

I was modifying some command line parameters, but it returns the same error with parameter -a with the known protein coding annotation. -g custom_GTF -a gencode_GTF: This fails -g gencode_GTF...

I think it would be helpful if I can have that parameter added in. Thank you so much!

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...

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