Elementolab/DataVisualization

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	-showwigtags 0 -output bed -uniq 1 > s_3_sequence.txt.noadapt.sorted.bam.100k.bed		-showwigtags 0 -output bed -uniq 1 > s_3_sequence.txt.noadapt.sorted.bam.100k.bed
	perl ~/PERL_SCRIPTS/circos_run.pl --bedfile=s_3_sequence.txt.noadapt.sorted.bam.100k.bed --genome=mm9 --outfile=F10-1ds.png --title=F10-1ds		perl ~/PERL_SCRIPTS/circos_run.pl --bedfile=s_3_sequence.txt.noadapt.sorted.bam.100k.bed --genome=mm9 --outfile=F10-1ds.png --title=F10-1ds
		+
		+	* uploading BAM tracks to UCSC GB
		+
		+	track type=bam name="F10-1ds" bigDataUrl=http://physiology.med.cornell.edu/faculty/elemento/lab/files/s_1_sequence.txt.noadapt.sorted.bam

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Revision as of 23:11, 24 March 2012

• Circos tutorial http://mkweb.bcgsc.ca/dev/circos/documentation/tutorials/2d_tracks/histograms/lesson/
• How to add a title to a Circos plot http://www.imagemagick.org/Usage/annotating/#anno_on
• Circos mailing list http://groups.google.com/group/circos-data-visualization

• Simple Perl script to generate Circos plot from bed file (in PERL_SCRIPTS in svn), based on Template Toolkit http://template-toolkit.org/docs/tutorial/Datafile.html

~/PROGRAMS/SNPseeqer/MakeGenomicTrackFromSortedBAMFile -bamfile s_3_sequence.txt.noadapt.sorted.bam -ws 100000 \
   -chrdata /home/ole2001/PROGRAMS/SNPseeqer/REFDATA/mm9.chrdata -normalize 1 -normto 100000000 -allpos 1 \
   -showwigtags 0 -output bed -uniq 1 > s_3_sequence.txt.noadapt.sorted.bam.100k.bed
perl ~/PERL_SCRIPTS/circos_run.pl --bedfile=s_3_sequence.txt.noadapt.sorted.bam.100k.bed --genome=mm9 --outfile=F10-1ds.png --title=F10-1ds

• uploading BAM tracks to UCSC GB

track type=bam name="F10-1ds" bigDataUrl=http://physiology.med.cornell.edu/faculty/elemento/lab/files/s_1_sequence.txt.noadapt.sorted.bam