Hi First of all thanks for looking into my post. I was wondering if I have the transcript IDs extracted from the cufflinks output (transcripts.gtf), is it possible to find whether the transcripts are coding or non-coding and if they are ncRNA, if they are pseudogenes or snoRNA or miRNA or other types of ncRNA.
Is there any online bioinformatics tool available to detect the biotype of transcripts.
These are few of my sample transcript IDs :
ENST00000492842
ENST00000492842
ENST00000410691
ENST00000410691
ENST00000493797
ENST00000493797
ENST00000493797
ENST00000496488
ENST00000496488
ENST00000496488
ENST00000458203
ENST00000458203
Any help in this regard will be highly appreciated. Thanks in advance.
GTF file used for cufflinks should provide you with the "biotype" information
For example: Ensemble Homo_sapiens GRCh37 71 GTF file
11 snRNA exon 10420739 10420864 . - . gene_id "ENSG00000221574"; transcript_id "ENST00000408647"; exon_number "1"; gene_name "U6atac"; gene_biotype "snRNA"; transcript_name "U6atac.23-201"; exon_id "ENSE00001565282";
11 snoRNA exon 10823014 10823155 . - . gene_id "ENSG00000238622"; transcript_id "ENST00000459187"; exon_number "1"; gene_name "SNORD97"; gene_biotype "snoRNA"; transcript_name "SNORD97-201"; exon_id "ENSE00001806941";
Than map each transcript or gene with its biotype.
quick awk script: save it as get.gtf.ensg.biotypes.awk
BEGIN {OFS=FS="\t"}
(substr($1,1,1)!="#" && substr($1,2,1)!="#") {
split($9,format,";");
i=0;
for (i in format){
if (format[i] ~ /gene_biotype|gene_type/){
gsub("gene_biotype | gene_type ", "", format[i]);
gsub(/"/,"",format[i]);
gsub(/gene_id "/,"",format[1]);
gsub(/transcript_id "/,"",format[2]);
gsub(/"/,"",format[1]);
gsub(/"/,"",format[2]);
#print format[1] "\t" format[i];
print format[1] "\t" format[2] "\t" format[i];
}
}
}
Run it:
awk -f get.gtf.ensg.biotypes.awk Homo_sapiens.GRCh37.71.gtf
Sample out put:
ENSG00000210049 ENST00000387314 Mt_tRNA
ENSG00000211459 ENST00000389680 Mt_rRNA
ENSG00000210077 ENST00000387342 Mt_tRNA
ENSG00000210082 ENST00000387347 Mt_rRNA
ENSG00000209082 ENST00000386347 Mt_tRNA
ENSG00000198888 ENST00000361390 protein_coding
ENSG00000198888 ENST00000361390 protein_coding
ENSG00000210100 ENST00000387365 Mt_tRNA
ENSG00000210107 ENST00000387372 Mt_tRNA
ENSG00000210112 ENST00000387377 Mt_tRNA
ENSG00000198763 ENST00000361453 protein_coding
ENSG00000198763 ENST00000361453 protein_coding
.....
Those are all Ensembl transcript IDs. You can look up all the information about them on Ensembl Genome Browser. Example: http://uswest.ensembl.org/Homo_sapiens/Search/Details?db=core;end=1;idx=Gene;q=ENST00000492842;species=Homo_sapiens
Thanks Rm and jxchong for your replies. I really appreciate it.
The awk script is awesome - though I have a question - in the 9th column of the GTF file, do we gene biotype or transcript biotype.
Pardon my ignorance - is it possible for transcripts to have different biotype from its corresponding gene,
Like for example - if Gene abc is miRNA - and say if it has three transcripts, can the biotype for these 3 transcripts be miRNA, protein_coding and snoRNA or do you think all the three transcripts will be miRNA only ? Please suggest.
Thanks once again for your time on this.
Yes, a gene can have both coding and non coding transcripts. It's unlikely that there will be three different "active" transcript types from a single gene, but you can certainly get, for example, protein_coding and processed_transcript. For example: http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000121879;r=3:178865902-178957881
This gene has four transcripts, three of which are coding and one is a retained intron.
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