Question: How to sort genes into coding and non-coding mRNA?
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gravatar for ag1805x
9 months ago by
ag1805x110
India
ag1805x110 wrote:

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.

sequencing rna-seq gene • 388 views
ADD COMMENTlink modified 9 months ago by h.mon21k • written 9 months ago by ag1805x110

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.

ADD REPLYlink written 9 months ago by cschu1811.4k

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

ADD REPLYlink written 9 months ago by ag1805x110
1

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

ADD REPLYlink written 9 months ago by cschu1811.4k
3
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