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Salmon: indexing genome and transcriptome

    • Closed Issue created by BIOPZ-Bak Maciej @bakma

    With salmon 1.0.0+ we should prepare and index genome+transcriptome in the following manner:
    https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/

    Please take a look here: https://www.biorxiv.org/content/10.1101/138800v2
    Authors also emphasize this on salmon gitter channel.

    Edit:

    That is also what they recommend in the docs (section 3.2):
    https://readthedocs.org/projects/salmon/downloads/pdf/latest/

    Edited
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