Using gtf file to get gene positions
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7 weeks ago
margo ▴ 40

Hi, I am wanting to extract gene positions from a gtf file using R. I have uploaded the gtf file as a df in R, with the headings 'seqnames', 'start', 'end', 'strand' and 'gene_id'. I am wanting to use this genome annotation to get the gene positions. Does anyone know a way I can do this on R.

My desired output would produce the different gene positions from the gtf file.

gtf igv bioinformatics R sequencing • 167 views
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3
Entering edit mode
7 weeks ago
ahmad mousavi ▴ 710

Hi

You should get subset of the data frame in another data frame, try like following for 3 column of it.

df2 <- unique( df[,c("start","end","gene_id")]) 
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