-a option

[bshim181]

Hello,

I have a custom stringtie derived GTFs that I am trying to predict ORFs from.

I am also inputting the primary assembly gene annotations from gencode with option -a

ribotish predict -b file1,2,3 -t file4,5,6 -a gencode.gtf -g custom.gtf -f $reference_assembly -o output.txt -v --seq --inframecount --altcodons ATG,CTG,GTG,TTG,ACG --minaalen 7

do you have an idea of why I might still encounter this error?

[zhpn1024]

What about the quality figure?

[bshim181]

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 \ --readFilesIn ${file} \ --outFilterMismatchNmax 2 \ --outFilterMultimapNmax 10 \ --outFilterMismatchNoverLmax 0.04 \ --alignIntronMin 20 \ --alignIntronMax 100000 \ --quantMode TranscriptomeSAM GeneCounts \ --alignSJDBoverhangMin 1 \ --outSAMattributes All \ --outSAMtype BAM SortedByCoordinate \ --sjdbGTFfile custom_gtf \ --outFileNamePrefix out_file done

I generated the bam file with star based on the custom gtf. do I have to align to the transcriptome?