Elementolab/DataVisualization

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 +* memory usage in generating UCSC big tracks
 +** 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]]
 +
* 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/
* How to add a title to a Circos plot http://www.imagemagick.org/Usage/annotating/#anno_on * How to add a title to a Circos plot http://www.imagemagick.org/Usage/annotating/#anno_on

Revision as of 16:04, 10 May 2012

~/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
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