Michael Love

Hello Mike,

I am trying to use DEseq2 for my zebrafish bulk-RNAseq data. I used Salmon to do the counting, and during that, I followed this tutorial to build the Salmon index (https://combine-lab.github.io/alevin-tutorial/2019/selective-alignment/), where I used both cdna and genome fasta files.

I wonder if you could clarify for me if this Salmon index should be used for tximeta makeLinkTome? And if I should put links of the cdna and genome fasta files in the function?

Thank you! Jing

Exactly (point to the Salmon index using makeLinkedTxome, and you can provide just the cDNA fasta, as you are only specifying the txps used for quantification). Let me know how it goes.