How to sort genes into coding and non-coding mRNA?

Question

[Arindam Ghosh]

I have a set of differentially expressed genes after analysis of RNAseq data. How can I sort them into protein coding genes and miRNA, ncRNA? I have used HISAT2-STRINGTIE-BALLGOWN for analysis. Reference genome: GRCh38 with annotation from Ensembl release 84.

[cschu181]

Translate + blastp or blastx against a proteome. Stuff that does match: proteins, stuff that does not match: either novel proteins (check for ORFs) or ncRNA. The ncRNA candidates you could check against Rfam, e.g. with Infernal.

[Arindam Ghosh]

That will be a tedious task as I have ~2000 of GENE names and Ids.

[cschu181]

I am not talking about using blast manually via web interface ;P

Answer 1

[h.mon]

Colsult our ancestors wisdom:

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