How to create a GRangesList object for genome not from UCSC?

dicty · 02-15-2011, 08:09 AM

Hi,

I just downloaded a virus genome and the annotation file from NCBI, but not UCSC. How to create a GRangesList object with the virus genome sequence and annotation file that are not from UCSC?

Thanks,

Dicty

robsyme · 02-15-2011, 04:32 PM

If you are able to get the gene starts, stops, chromosome, etc into vectors this gist might be helpful:

https://gist.github.com/660729

dicty · 02-16-2011, 07:51 AM

Thanks a lot.

Actually I'd like to make a TranscriptDb object, but not sure how to do it.

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02-15-2011, 08:09 AM	#1
dicty Member Location: us Join Date: Nov 2010 Posts: 28	How to create a GRangesList object for genome not from UCSC? Hi, I just downloaded a virus genome and the annotation file from NCBI, but not UCSC. How to create a GRangesList object with the virus genome sequence and annotation file that are not from UCSC? Thanks, Dicty

02-15-2011, 04:32 PM	#2
robsyme Junior Member Location: Perth, Western Australia Join Date: Jan 2009 Posts: 6	If you are able to get the gene starts, stops, chromosome, etc into vectors this gist might be helpful: https://gist.github.com/660729

02-16-2011, 07:51 AM	#3
dicty Member Location: us Join Date: Nov 2010 Posts: 28	Thanks a lot. Actually I'd like to make a TranscriptDb object, but not sure how to do it.