17 July 2010
Hi Shaun,

I've dug out the v1.1.1 contigs corresponding to the example events we 
used for the manuscript (there may be a few more coming).
The lists are in 
/projects/morgen/wtss_assembly/MM0472/assembly2/abyss-1.1.1/novelty/*.txt.
Inside each file are the contig numbers.

The data files are all in 
/projects/morgen/wtss_assembly/MM0472/assembly2/abyss-1.1.1/

Merged contigs: merge/MM0472-main.fa

Tracks:
tracks/MM0472.merge.main-nou.best.unique.m90.blat.psl
tracks/MM0472.merge.main-nou.best.unique.m90.blat.psl

Exonerate alignments:
merge/pe_contig_aligns/mm9/exonerate_2.2/MM0472.merge.main.mm9.exon
Blat alignments:
merge/pe_contig_aligns/mm9/exonerate_2.2/MM0472.merge.main.mm9.psl

thanks,
Readman

17 July 2010: copy tracks from /projects/morgen/... to /projects/remc_bigdata/MORGEN/...
cp /projects/morgen/wtss_assembly/MM0472/assembly2/abyss-1.1.1/tracks/MM0472.merge.main-nou.best.unique.m90.* .

[grobertson@xhost09 tracks]$ pwd
/projects/remc_bigdata/MORGEN/MM0472_WTSS_liver_adult/abyss_1.1.1/tracks
[grobertson@xhost09 tracks]$ ll -h
total 188M
-rw-r--r-- 1 grobertson users 2.6M Jul 15 15:02 MM0472.merge.adj-nou.best.unique.m90.blat.psl
-rw-r--r-- 1 grobertson users 4.8M Jul 15 15:02 MM0472.merge.adj-nou.best.unique.m90.exon.gff
-rw-r--r-- 1 grobertson users  89M Jul 17 14:04 MM0472.merge.main-nou.best.unique.m90.blat.psl
-rw-r--r-- 1 grobertson users  91M Jul 17 14:04 MM0472.merge.main-nou.best.unique.m90.exon.gff
-rw-r--r-- 1 grobertson users  925 Jul 17  2010 readme.txt

Gzip these files
[grobertson@xhost09 tracks]$ ll -h
total 55M
-rw-r--r-- 1 grobertson users 1.1M Jul 15 15:02 MM0472.merge.adj-nou.best.unique.m90.blat.psl.gz
-rw-r--r-- 1 grobertson users 1.1M Jul 15 15:02 MM0472.merge.adj-nou.best.unique.m90.exon.gff.gz
-rw-r--r-- 1 grobertson users  27M Jul 17 14:04 MM0472.merge.main-nou.best.unique.m90.blat.psl.gz
-rw-r--r-- 1 grobertson users  26M Jul 17 14:04 MM0472.merge.main-nou.best.unique.m90.exon.gff.gz
-rw-r--r-- 1 grobertson users 3.7K Jul 17 14:10 readme.txt


Try to load these from the http-addressable folder.
Remember how we did this - look on the MORGEN wiki -
http://www.bcgsc.ca/wiki/display/Morgen/Resources+for+novel+events
New bigWig
browser position chr1:183023510-183023609
track type=bigWig name=MM0472_wtss description="MM0472 WTSS: adult liver, 20100508" color=50,50,150 maxHeightPixels=40:40:20 db=mm9 alwaysZero=on visibility=full priority=79 bigDataUrl=http://www.bcgsc.ca/downloads/genereg/remcbigdata/MORGEN/MM0472_WTSS_liver_adult/MM0472.merged_7_lanes_withJunctionsOnGenome_dupsFlagged.pileup.bw

http://www.bcgsc.ca/downloads/genereg/remcbigdata/MORGEN/MM0472_WTSS_liver_adult/abyss_1.1.1/tracks/MM0472.merge.main-nou.best.unique.m90.blat.psl.gz
http://www.bcgsc.ca/downloads/genereg/remcbigdata/MORGEN/MM0472_WTSS_liver_adult/abyss_1.1.1/tracks/MM0472.merge.main-nou.best.unique.m90.exon.gff.gz
http://www.bcgsc.ca/downloads/genereg/remcbigdata/MORGEN/MM0472_WTSS_liver_adult/abyss_1.1.1/tracks/MM0472.merge.adj-nou.best.unique.m90.blat.psl.gz
http://www.bcgsc.ca/downloads/genereg/remcbigdata/MORGEN/MM0472_WTSS_liver_adult/abyss_1.1.1/tracks/MM0472.merge.adj-nou.best.unique.m90.exon.gff.gz

http://www.bcgsc.ca/downloads/genereg/wtss_assy/H3K4me3_MM0281_1L_mm9_xset200_dupsN_ht3.wig.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/ssoohe_mm0280.sagelib_f.wig
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/ssoohe_mm0280.sagelib_r.wig

http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/mm9Mus_musculusAntisense_ncRNA_Pipeline.bed
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/mm9Mus_musculusFantom3.bed

OLD tracks
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.main.best.unique.m90.blat.psl.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.main.best.unique.m90.blat.snv.gff.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.adj.best.unique.m90.blat.psl.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.adj.best.unique.m90.blat.snv.gff.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.main.best.unique.m90.exon.gff.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.main.best.unique.m90.exon.snv.gff.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.adj.best.unique.m90.exon.gff.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/MM0472.merge.adj.best.unique.m90.exon.snv.gff.gz
http://www.bcgsc.ca/downloads/genereg/wtss_assy/MM0472.merge.main.best.unique.m90.gmap.psl
http://www.bcgsc.ca/downloads/genereg/wtss_assy/20100407/events_main.v306.bed