Comments (3)
From the file names, I can see that you mapped the reads to transcriptome. In that pipeline, Salmon is used to estimate the abundance of transcripts and then tximport is used to obtain the gene abundance from its relevant transcripts. In that case, as Salmon
puts on its website "Don't count . . . quantify!" it produces estimation instead of real count.
If you want to get the genes' read counts, I suggest to go for the other pipeline "genome" as shown in theworkflowchart
from rasflow.
Thanks for your reply. I will try the genome
option. You can close the issue then.
from rasflow.
Will close it for now. Don't hesitate to reopen it if you encounter further issues on the genome
pipeline.
from rasflow.
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from rasflow.