Elementolab/DataVisualization

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	* memory usage in generating UCSC big tracks		* memory usage in generating UCSC big tracks
	** in general http://genomewiki.ucsc.edu/index.php/Big_file_converters		** in general http://genomewiki.ucsc.edu/index.php/Big_file_converters
-	** following this [[https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025335.html post]], we made a version of bedGraphToBigWig with memory limit of 64Gb that can be downloaded [[http://physiology.med.cornell.edu/faculty/elemento/lab/public_download/bedGraphToBigWig here]]	+	** following this [[https://lists.soe.ucsc.edu/pipermail/genome/2011-March/025335.html post]], we made a version of bedGraphToBigWig (and other big file converters) with memory limit of 64Gb that can be downloaded [[http://physiology.med.cornell.edu/faculty/elemento/lab/public_download/big_ucsc here]]
	* Circos tutorial http://mkweb.bcgsc.ca/dev/circos/documentation/tutorials/2d_tracks/histograms/lesson/		* Circos tutorial http://mkweb.bcgsc.ca/dev/circos/documentation/tutorials/2d_tracks/histograms/lesson/

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Current revision

• memory usage in generating UCSC big tracks
  • in general http://genomewiki.ucsc.edu/index.php/Big_file_converters
  • following this [post], we made a version of bedGraphToBigWig (and other big file converters) with memory limit of 64Gb that can be downloaded [here]

• 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 visibility=squish