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alexdobin / STAR

RNA-seq aligner

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thoughts on STAR development team on splice/unsplice/ambigiuous reads classification.

mortunco opened this issue · comments

commented

Dear @alexdobin

This is not an issue but rather asking your thoughts about recent manuscripts about splice/unsplice/ambiguous read classification. I am sure you are reading on this but havent seen a discussion in the repository. If there has one before, I am sorry for that.

The chronology of my references might be wrong but lets use them as sources of the general concepts. (some preprints got updated)

  1. (Soneson et al 2021) https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008585
    This publication demonstrated Kallisto/Alevin/STARsolo generated different count tables hence they generate different velocity calculation. The problem is due to low read length makes ambiguous reads very hard to classify.

  2. (He et al, 2023) https://www.biorxiv.org/content/10.1101/2023.01.04.522742v1.full.pdf and (Hjörleifsson and Sullivan et al, 2024) www.biorxiv.org/content/10.1101/2022.12.02.518832v3.full.pdf utilized flanking k-mers to a rescue a read from ambiguity to and assign to spliced/unspliced.

The reason i am asking is both of the publications always adds STAR into their comparison so I want to hear your opinion about full transcriptome quantification. What are your thoughts on issue? Are you planning to come up with a update in the algorithm on this? Velocyto option in STAR solo is my goto option for spliced/unspliced counts but do you have suggestions to improve accuracy of the quantification with STAR ?

Thank you for maintaining STAR. Its very easy to use which makes it extremely useful. Thank you very much for your time,

Best,
T.

commented

Hello! I am a primary author on one of the listed preprints (and am an avid STARsolo user+fan too despite much of my work being done using pseudoalignment) -- thanks for reading my preprint! :) And thanks to Dr. Dobin for his great work on STAR of course. I am posting here to bookmark this discussion and to potentially engage in it further.