Retrieve information on gff files

[tindinh]

Hi guys,

I wanna extract information on gff files to set the input for CVNrd2 package running. I want the information about chr start and end, gene names and their start and end position for Illumina dataset.

I am trying rtracklayer but I seem only good for Affix data. Can you recommend me some?

Thank you!

[dpryan]

You might find it easier to use GenomicFeatures. You can construct a TranscriptDb with makeTranscriptDbFromGFF(). Then you can simply genes(txdb) to get the gene coordinates and names.

[tindinh]

it's very helpful. Thank you!

[tindinh]

You might find it easier to use GenomicFeatures. You can construct a TranscriptDb with makeTranscriptDbFromGFF(). Then you can simply genes(txdb) to get the gene coordinates and names.

But I might need to convert gff to gff3 files, right? If so, how can I do that?
Thank you!

[dpryan]

It's very likely that your gff file is a gff3 file, ignore the extension.

[tindinh]

It's very likely that your gff file is a gff3 file, ignore the extension.

Nope, I checked it's gff not gff3.

[dpryan]

If you google around you can find some programs to convert gff to gff3. There's no standard way to do this, since gff isn't a well specified format.