Pseudodomonas syringae - Revision history

Dpuiu: /* UNC: Jeff Dangl */

2008-05-28T17:16:20Z

UNC: Jeff Dangl

← Older revision		Revision as of 17:16, 28 May 2008
Line 46:		Line 46:
	454p		454p
	* Out of 123992 454 paired ends, 111028 (90%) align to linker (nucmer -c 20 -l 20)		* Out of 123992 454 paired ends, 111028 (90%) align to linker (nucmer -c 20 -l 20)
	* Non ~~linker~~ sequences (5' & 3')		* Non linked(end) sequences (5' & 3')
	#elem min max mean median n50 sum		#elem min max mean median n50 sum
	five 111028 0 265 37 21 61 4090475		five 111028 0 265 37 21 61 4090475
Line 52:		Line 52:

	* 20bp is the mode		* 20bp is the mode
			* 75% of the end sequences are 19-21 bp long
			* 67871 out of 111028 end pairs align within 5kbp
			#elem min max mean stdev sum
			distance 67871 1 4991 2450 702 166283200

	UNC sequence data: (not avail any more?)		UNC sequence data: (not avail any more?)

2008-05-28T17:06:58Z

UNC: Jeff Dangl

← Older revision		Revision as of 17:06, 28 May 2008
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	Solexa DC3000.reads.filtered.fasta 6,340,136 32 32 32 202884352 32 0 32		Solexa DC3000.reads.filtered.fasta 6,340,136 32 32 32 202884352 32 0 32
	454p(end+linker) DC3000.format.454Reads.fna 123,992 38 86 329 15623908 126.01 58.89 142		454p(end+linker) DC3000.format.454Reads.fna 123,992 38 86 329 15623908 126.01 58.89 142
	~~454p(ends) . 247,984 1 21 317 14065098 57 .~~		454 DC3000.TCA.454reads.format.fna 77,466 35 244 371 18627363 240.46 26.85 245
	454 DC3000.TCA.454reads.format.fna 77,466 35 244 371 18627363 240.46 26.85 245

	* Solexa 3 lanes;		* Solexa 3 lanes;
Line 44:		Line 43:
	Quality values are missing for all data sets!!!		Quality values are missing for all data sets!!!
	I assigned default qual=3 to all the base (.frg & .afg files) </span>		I assigned default qual=3 to all the base (.frg & .afg files) </span>

			454p
			* Out of 123992 454 paired ends, 111028 (90%) align to linker (nucmer -c 20 -l 20)
			* Non linker sequences (5' & 3')
			#elem min max mean median n50 sum
			five 111028 0 265 37 21 61 4090475
			three 111028 0 266 39 20 81 4385391

			* 20bp is the mode


	UNC sequence data: (not avail any more?)		UNC sequence data: (not avail any more?)

2008-05-20T01:04:47Z

UNC: Jeff Dangl

← Older revision		Revision as of 01:04, 20 May 2008
Line 28:		Line 28:
	Read stats		Read stats

	Type File #reads min median max sum mean stdev n50		Type File #reads min median max sum mean stdev n50
	Solexa DC3000.reads.filtered.fasta 6,340,136 32 32 32 202884352 32 0 32		Solexa DC3000.reads.filtered.fasta 6,340,136 32 32 32 202884352 32 0 32
	454p DC3000.format.454Reads.fna 123,992 38 86 329 15623908 126.01 58.89 142		454p(end+linker) DC3000.format.454Reads.fna 123,992 38 86 329 15623908 126.01 58.89 142
	454 DC3000.TCA.454reads.format.fna 77,466 35 244 371 18627363 240.46 26.85 245		454p(ends) . 247,984 1 21 317 14065098 57 .
			454 DC3000.TCA.454reads.format.fna 77,466 35 244 371 18627363 240.46 26.85 245

	* Solexa 3 lanes;		* Solexa 3 lanes;

2008-02-29T18:48:33Z

454 + Solexa AMOScmp

← Older revision		Revision as of 18:48, 29 February 2008
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	=== 454 + Solexa AMOScmp ===		=== 454 + Solexa AMOScmp ===

			Locations:
			/fs/szasmg2/Bacteria/Pseudomonas_syringae/Assembly/Solexa-454/2008_1016_AMOSCmp-relaxed/
			ftp://ftp.cbcb.umd.edu/pub/data/dpuiu/Pseudomonas_syringae/Solexa-454/

	AMOScmp -D MINCLUSTER=20 -D MAXTRIM=20 -D MINOVL=5 -D MAJORITY=50 -D ALIGNWIGGLE=2 ...		AMOScmp -D MINCLUSTER=20 -D MAXTRIM=20 -D MINOVL=5 -D MAJORITY=50 -D ALIGNWIGGLE=2 ...

2008-02-29T18:16:43Z

454 + Solexa AMOScmp

← Older revision		Revision as of 18:16, 29 February 2008
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	AMOScmp -D MINCLUSTER=20 -D MAXTRIM=20 -D MINOVL=5 -D MAJORITY=50 -D ALIGNWIGGLE=2 ...		AMOScmp -D MINCLUSTER=20 -D MAXTRIM=20 -D MINOVL=5 -D MAJORITY=50 -D ALIGNWIGGLE=2 ...

	~~Stats~~:		All stats:
	desc #elem min max mean stdev sum		desc #elem min max mean stdev sum
	contigs 139 20 1895644 46899.82 243273.92 6519075		contigs 139 20 1895644 46899.82 243273.92 6519075
	pos_gaps 124 1 1809 156.78 323.66 19441		pos_gaps 124 1 1809 156.78 323.66 19441

			Chromosome stats:
			desc #elem min max mean stdev sum
			contigs 8 85757 1895607 799498.75 692179.25 6395990
			pos_gape 2 4 9 6.5 3.53 13

	=== 454 + Solexa + 454p AMOScmp ===		=== 454 + Solexa + 454p AMOScmp ===

2008-02-29T17:49:57Z