Francisella tularensis tularensis ATCC6223: Difference between revisions

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


== Data ==  
== Data ==  


'''Reference:'''


'''Libraries:'''
'''Libraries:'''


   CENTER  PROJECT STRAIN   LIB                TYPE  SIZE  STDEV    COUNT  LOCATION
   CENTER  PROJECT STRAIN   LIB                TYPE  SIZE  STDEV    COUNT  LOCATION
   BCM      BFTF          ATCC6223  BFTFP              WGS    6,250  1,250    2,144  TA
   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_000SA  454    .      .      408,780  TA
Line 19: Line 18:
   /fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/
   /fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/


'''2007_0821_454'''
'''2007_0821_AMOScmp-454 -> best'''
newbler assembly of 4WG_FTUL.AT_000pA
  => 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp
   /fs/sz-user-supported/Linux-x86_64/packages/rig -> rig_1.1.01.20/
   272,522 singletons ; all 454 paired reads are left as singletons
   $ newAssembly 2007_0821_454
 
   $ addRun 2007_0821_454/ *sff
'''2007_0821_AMOScmp-454-SchuS4'''
   $ cd 2007_0821_454
  uses Schu S4 (complete) as reference
   $ runProject
  => 1 scaff, 194 contigs, 1,759,427 bp
   # 0 overlaps => 0 contigs ???
  => 2 large areas with coverage twice as deep as average
  => 3 large areas with no 454 coverage
 
'''2007_0821_AMOScmp-454-FSC198'''
  uses FSC198 (complete) as reference
  => 1 scaff, 195 contigs, 1,761,838 bp
   => 2 large areas with coverage twice as deep as average
   => 3 large areas with no 454 coverage
 
'''2007_0821_AMOScmp-454-WY96-3418'''
   uses  WY96-3418(complete) as reference
   => 1 scaff, 144 contigs, 1,761,838 bp
  => 2 large areas with coverage twice as deep as average
   => 4-5 large areas with no 454 coverage
 
 
'''Problem'''
  lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; could not run newbler on both 454 libraries

Latest revision as of 20:23, 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_AMOScmp-454 -> best

 => 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp
 272,522 singletons ; all 454 paired reads are left as singletons

2007_0821_AMOScmp-454-SchuS4

 uses Schu S4 (complete) as reference
 => 1 scaff, 194 contigs, 1,759,427 bp
 => 2 large areas with coverage twice as deep as average
 => 3 large areas with no 454 coverage

2007_0821_AMOScmp-454-FSC198

 uses FSC198 (complete) as reference
 => 1 scaff, 195 contigs, 1,761,838 bp
 => 2 large areas with coverage twice as deep as average
 => 3 large areas with no 454 coverage

2007_0821_AMOScmp-454-WY96-3418

 uses  WY96-3418(complete) as reference
 => 1 scaff, 144 contigs, 1,761,838 bp
 => 2 large areas with coverage twice as deep as average
 => 4-5 large areas with no 454 coverage


Problem

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