Re: [galaxy-user] Galaxy Reference Genome

2012-06-14 Thread Loraine, Ann
option. (Maybe it already does?) GTF is an awkward format and BED would work just as well, if not better. Best wishes, Ann Loraine --- Ann Loraine, Ph.D. Associate Professor Department of Bioinformatics and Genomics University of North Carolina at Charlotte North Carolina

Re: [galaxy-user] Downloading the gene coordinates of the rice genome

2012-12-10 Thread Loraine, Ann
Hello, This may be useful: Integrated Genome Browser (the display in IGB link) has gene models for IRG4.0 in BED format: http://www.igbquickload.org/quickload/O_sativa_japonica_Jun_2009/O_sativa_japonica_Jun_2009.bed.gz The original data were taken from Phytozome.net and reformatted to BED.

Re: [galaxy-user] identify different number of differential expressed genes using ensemble or reseq GTF

2013-01-08 Thread Loraine, Ann
! Best wishes, Ann Loraine --- Ann Loraine, Ph.D. Associate Professor Department of Bioinformatics and Genomics University of North Carolina at Charlotte North Carolina Research Campus 600 Laureate Way Kannapolis, NC 28081 704-250-5750 alora...@uncc.edu http

Re: [galaxy-user] FastQC Issue with per base nucleotide quality graph

2013-03-28 Thread Loraine, Ann
What does it tell you about the number of N's (uncalled bases)? From: Tan, Justin j...@fas.harvard.edumailto:j...@fas.harvard.edu Date: Thu, 28 Mar 2013 10:41:24 -0400 To: galaxy-user@lists.bx.psu.edumailto:galaxy-user@lists.bx.psu.edu