I have two species RNA sequencing data, species A and B. the normal analysis was almost done, I got some key genes and now I want to see the expression value of these genes, and eliminate the genes that have low expression value (these genes may not play an important role in this species development).
species A haven't had a reference genome, so I used the
1.Trinity 2.align_and_estimate_abundance.pl 3.abundance_estimates_to_matrix.pl then I got a file called
rsem-gene.isoform.TPM.not_cross_norm, I want to know if this file can be thought the expression value for the genes in species A? if yes, if there is any cutoff value for us to say the expression value if low?
And species B had a reference genome, so I used
STAR-HTSeq-DEseq2, there is one step in DEseq2
normalized_counts <- counts(dds, normalized=TRUE)can do the normalization, so I want to know for species B, if this is the expression value? if yes, the cutoff should be what,,,
Thanks in advance!