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pachterlab / kallisto

Near-optimal RNA-Seq quantification
https://pachterlab.github.io/kallisto
BSD 2-Clause "Simplified" License
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How to construct and index file with extended TTS #322

Open bweatherbee opened 3 years ago

bweatherbee commented 3 years ago

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 commented 3 years ago

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