What is your organism model?
If you are using some genome from ensembl, and used the gtf file with the set of anotations in the HTSeq-count, you can import all the tables with counts in txt files inside a data.frame in R.
with bioconductor do:
with this package you can get from the ensembl, a dataset based in several filters, for example, the biotype ( if it is coding or noncoding.)
Then you can simple merge the two tables based in the ensembl ID's and separate them based in your criteria. If you do not want to use R, the ensemble has a graphic web interface in http://www.ensembl.org/biomart, although I recommend R, because will be more easy later to create better graphics and statistics.
ps: biomaRt also can handle Uniprot and HapMap databases