Francisella tularensis tularensis ATCC6223 - Revision history

Dpuiu at 20:23, 23 August 2007

2007-08-23T20:23:13Z

← Older revision		Revision as of 20:23, 23 August 2007
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)

2007-08-23T20:22:58Z

← Older revision		Revision as of 20:22, 23 August 2007
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	'''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

2007-08-23T20:22:00Z

Assembly

← Older revision		Revision as of 20:22, 23 August 2007
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	'''2007_0821_AMOScmp-454-SchuS4'''		'''2007_0821_AMOScmp-454-SchuS4'''
	uses Schu S4 as reference		uses Schu S4 (complete) as reference
	=> 1 scaff, 194 contigs, 1,759,427 bp		=> 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'''		'''Problem'''
	lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; could not run newbler on both 454 libraries		lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; could not run newbler on both 454 libraries

2007-08-23T20:12:23Z

Assembly

← Older revision		Revision as of 20:12, 23 August 2007
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 21:		Line 21:
	=> 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp		=> 88 scaffolds, 188 contigs, 1,762,423 bp ; maxContigLen=70,372 bp
	272,522 singletons ; all 454 paired reads are left as singletons		272,522 singletons ; all 454 paired reads are left as singletons

			'''2007_0821_AMOScmp-454-SchuS4'''
			uses Schu S4 as reference
			=> 1 scaff, 194 contigs, 1,759,427 bp

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

2007-08-23T14:44:34Z

← Older revision		Revision as of 14:44, 23 August 2007
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)

2007-08-23T14:44:26Z

← Older revision		Revision as of 14:44, 23 August 2007
Line 20:		Line 20:
	'''2007_0821_AMOScmp-454 -> best'''		'''2007_0821_AMOScmp-454 -> 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
			272,522 singletons ; all 454 paired reads are left as singletons

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

2007-08-23T14:37:40Z

Assembly

← Older revision		Revision as of 14:37, 23 August 2007
Line 18:		Line 18:
	/fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/		/fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/

	'''2007_0821_AMOScmp -> best'''		'''2007_0821_AMOScmp-454 -> 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'''		'''Problem'''
	lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; could not run newbler on both 454 libraries		lib 4WG_FTUL.AT_000SA in TA but not in SRA, .sff file is missing; could not run newbler on both 454 libraries

2007-08-23T14:35:05Z

Assembly

← Older revision		Revision as of 14:35, 23 August 2007
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 17:		Line 17:
	'''Locations:'''		'''Locations:'''
	/fs/szasmg2/Bacteria/F_tularensis_tularensis_ATCC6223/		/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'''		'''2007_0821_AMOScmp -> best'''

2007-08-23T14:34:14Z

← Older revision		Revision as of 14:34, 23 August 2007
Line 31:		Line 31:

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

2007-08-23T13:48:23Z

← Older revision		Revision as of 13:48, 23 August 2007
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