could I use cell deconvolution tools (like CIBERSORT) in 3'quantseq data?

Question

[eridanus]

Hello. I would like to ask if I could use CIBERSORT(with the LM22 signature matrix) or XCELL in 3'quantseq data? Thank you!

[ATpoint]

For the sake of providing a comment, the information you give are not sufficient to answer. Usually it is the number of samples, quality, presence of batch effects, composition etc. that tells whether you can or cannot use a certain tool, not the specific kit that was used to produce the samples.

[eridanus]

Thank you for your answer! I have 12 samples, no batch effects. RIN was not that good, that is the reason why 3'quantseq instead of total rnaseq was applied. When I run Cibersort, CibersortX, Xcell, p-values are > 0.05.