On 2010-06-11, Karen Mungall wrote...
Hi Shaun,

Here are some coordinates for the genome assemblies:

NBL01  (HS1194) 2 duplications and an inversion event affecting NBAS:
chr2:15,121,000-17,220,000

NBL10 (HS1803) 2 deletion events found affecting NBAS
chr2:12,500,000-15,700,000

NBL09 (HS1801) inversion affecting MPRIP
chr17:2,360,000-17,040,000

NBL07 (HS1797) deletion affecting LSAMP and STAG1
chr3:116,900,000-137,960,000

NBL06 (HS1795) translocation between chr11 and chr17 affecting RNF121 and TRIM37
chr17:53,962,000-54,860,000
chr11:70,860,000-71,815,000

NBL04 (HS1197) 2 Inversion events affecting RERE
chr1:4,175,500-9,251,000

NBL03 (HS1196) translocation event between chr 1 and chr22 affecting SAPS2 and SMYD3
chr22:48,845,000-49,540,000
chr1:243,804,000-245,422,000

Please let me know if you need anything else.

Thanks
Karen

On 2010-06-11, Karen Mungall wrote...
Hi Shaun,

Here are the libraries linked to the relevant samples:

NBL01 
HS1599 (germline)
HS1780

NBL02
HS1600 (germline)
HS1781

NBL03
HS1601 (germline)
HS1782

NBL04 (germline)
HS1602
HS1783

NBL05
HS1603 (germline)
HS1784

NBL06
HS1884 (germline)
HS1794

NBL07
HS1885 (germline)
HS1796

NBL08
HS1886 (germline)
HS1798

NBL09
HS1887 (germline)
HS1800

NBL10
HS1888 (germline)
HS1802


Thanks
Karen

On 2010-06-14, Richard Corbett wrote...
Hey Karen,

These are the NBL bam files.   NBL## are tumours, while NBL##G are normals:

/projects/rcorbettAlignment/NBL01/HS1780/31_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL02/HS1781/29_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL03/HS1782/30_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL04/HS1783/31_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL05/HS1784/30_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL06/HS1794/29_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL07/HS1796/29_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL08/HS1798/31_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL09/HS1800/27_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL10/HS1802/33_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL01G/HS1599/28_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL02G/HS1600/28_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL04G/HS1602/28_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL05G/HS1603/25_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL03G/HS1601/25_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL06G/HS1884/21_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL07G/HS1885/21_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL08G/HS1886/21_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL09G/HS1887/23_lanes.rmdup.bam
/projects/rcorbettAlignment/NBL10G/HS1888/21_lanes.rmdup.bam

Richard