Hello, I am trying to extract some transcript sequences from a stringtie merged gtf using gffread and am getting the following errors:
Error (GFaSeqGet): subsequence cannot be larger than 227 Error getting subseq for MSTRG.17.1 (1..229)!
This error happens for many of gene entries, some but not all transcripts end up getting extracted. The gtf file was created in StringTie using the same reference genome file as everything else (where my bam files are from, the reference annotation gtf file). This annotation is from running StringTie first and merging the gtf annotation files. The main problem seems to be that the end coordinates exceed sequence length when extracting transcripts even though I am sure that they were made correctly. If there is a way to just skip that particular gene that could work as well.
This is the command I used: gffread /Users/Desktop/StringTie_comp_annotation_new.gtf -g /Users/Desktop/Xla.v91.repeatMasked.fa -w transcripts.fasta