How to construct and index file with extended TTS

[bweatherbee]

I am trying to realign SC3 sequencing data from a published paper (method: https://pubmed.ncbi.nlm.nih.gov/25722368/), and it seems to do so they require the GTF/GFF3 file used for reference annotations to include a 10kb extension from the 3' TTS. Is this possible to build into the custom kb ref options? When I tried to do the realignment without this step, 0 pseudoalignments are found, so this does seem necessary. Thanks!

[Yenaled]

Can you show us the "kb ref" (index) and "kb count" (quantification) commands you're using?