SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Assisted de novo genome assembly? Create new consensus mapping reads to reference? zmartine Bioinformatics 8 02-10-2012 12:31 AM
how to create an annotation object dicty Bioinformatics 0 02-04-2011 10:33 AM
RNA-Seq: ENCODE whole-genome data in the UCSC genome browser (2011 update). Newsbot! Literature Watch 1 11-24-2010 01:08 PM
Create the best prokaryotic genome assembly: Combining different methods JurgenP Bioinformatics 4 02-27-2010 10:46 AM
UCSC Genome Browser ECHo Illumina/Solexa 0 02-25-2010 07:21 PM

Reply
 
Thread Tools
Old 02-15-2011, 07:09 AM   #1
dicty
Member
 
Location: us

Join Date: Nov 2010
Posts: 28
Default 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
dicty is offline   Reply With Quote
Old 02-15-2011, 03:32 PM   #2
robsyme
Junior Member
 
Location: Perth, Western Australia

Join Date: Jan 2009
Posts: 6
Default

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

https://gist.github.com/660729
robsyme is offline   Reply With Quote
Old 02-16-2011, 06:51 AM   #3
dicty
Member
 
Location: us

Join Date: Nov 2010
Posts: 28
Default

Thanks a lot.

Actually I'd like to make a TranscriptDb object, but not sure how to do it.
dicty is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 12:28 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO