Francisella tularensis tularensis ATCC6223: Difference between revisions

From Cbcb
Jump to navigation Jump to search
No edit summary
No edit summary
Line 1: Line 1:
Center: Baylor
  Center: Baylor
   Status: Assembly (88 contigs; 1,757,628 bp; maxLen=133,694 bp; avgLen=19,973 bp)
   Status: Assembly (88 contigs; 1,757,628 bp; maxLen=133,694 bp; avgLen=19,973 bp)


Line 27: Line 27:
   # 0 overlaps => 0 contigs ???
   # 0 overlaps => 0 contigs ???


'''2007_0821_AMOScmp'''
'''2007_0821_AMOScmp -> best'''
   => 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp
   => 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp
'''Problem'''
  lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; cound not run newbler on both 454 libraries

Revision as of 13:48, 23 August 2007

 Center: Baylor
 Status: Assembly (88 contigs; 1,757,628 bp; maxLen=133,694 bp; avgLen=19,973 bp)

Data

Libraries:

 CENTER   PROJECT	STRAIN	   LIB                TYPE   SIZE   STDEV    COUNT   LOCATION
 BCM      BFTF          ATCC6223  BFTFP              WGS    6,250  1,250     2,144  TA
 BCM      4WG_FTUL.AT   ATCC6223  4WG_FTUL.AT_000SA  454    .      .       408,780  TA
 BCM      4WG_FTUL.AT   ATCC6223  4WG_FTUL.AT_000pA  454    .      .       218,232  SRA ?
 Total                                                                     629,156

Assembly

Locations:

 /fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/

2007_0821_454

 newbler assembly of 4WG_FTUL.AT_000pA
 /fs/sz-user-supported/Linux-x86_64/packages/rig -> rig_1.1.01.20/
 $ newAssembly 2007_0821_454
 $ addRun 2007_0821_454/ *sff
 $ cd 2007_0821_454
 $ runProject
 # 0 overlaps => 0 contigs ???

2007_0821_AMOScmp -> best

 => 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp

Problem

 lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; cound not run newbler on both 454 libraries