Is RNA-Seq well suited for studying pseudogenes and lncRNA?

Question

[Kermit]

Previously (If RNA-seq includes miRNA genes then why are there miRNA specific pipelines?), I learned that it was bad form to retain miRNAs identified using RNA-Seq; miRNA should be identified using an miRNA-specific protocol.

Would the same statement apply to lncRNA and pseudogene transcripts, or is it okay to include them?

# Expression quantification of a given sample
protein_coding                        19962
lncRNA                                16901
processed_pseudogene                  10167
unprocessed_pseudogene                 2614

Answer 1

[rpolicastro]

lncRNAs are typically fine for downstream analysis as they are not excluded in most RNA-seq library preparations due to their length (>100 bp) and the presence of a polyA tail. I'm not sure how useful keeping pseudogenes would be outside of unique circumstances since by definition most are non-functional.