Pseudomonas aeruginosa - Revision history

Dpuiu: /* PA14 ref assembly (2) * */

2010-10-14T15:07:21Z

PA14 ref assembly (2) *

← Older revision		Revision as of 15:07, 14 October 2010
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	Total 7553734		Total 7553734

			<pre style="background:yellow">
	Contig stats:		Contig stats:
	desc #elem min max mean median n50 sum singl breaks		desc #elem min max mean median n50 sum singl breaks
	all 1843 20 127984 3350 63 30995 6174765 1107200 9		all 1843 20 127984 3350 63 30995 6174765 1107200 9
	200bp+ 542 200 127984 11245 3263 31106 6094904		200bp+ 542 200 127984 11245 3263 31106 6094904
			</pre>

	Alignment of contigs >=33bp to PA14 reference; qry_hits		Alignment of contigs >=33bp to PA14 reference; qry_hits

2010-10-12T20:09:27Z

AMOScmp on the velvet contigs & velvet singletons (PA14 ref) *

← Older revision		Revision as of 20:09, 12 October 2010
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	* This assembly will have some of the repeats collapsed		* This assembly will have some of the repeats collapsed

			<pre style="background:yellow">
	#elem min max mean median n50 sum		#elem min max mean median n50 sum
	all 2383 33 177630 2592 72 45071 6177155		all 2383 33 177630 2592 72 45071 6177155
Line 1,101:		Line 1,102:
	singl-velvet 984 45 16239 837 292 2221 823862 # velvet ctgs left as singletons		singl-velvet 984 45 16239 837 292 2221 823862 # velvet ctgs left as singletons
	singl-read 393416 33 45 33 33 33 12983724 # original Solexa reads not assembled		singl-read 393416 33 45 33 33 33 12983724 # original Solexa reads not assembled
			</pre>

	Location: /fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/Assembly/2008_0311_velvet-24/AMOScmp-PA14.singletons		Location: /fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/Assembly/2008_0311_velvet-24/AMOScmp-PA14.singletons

2010-10-12T20:08:20Z

Velvet *

← Older revision		Revision as of 20:08, 12 October 2010
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	contigs.fa : contig FASTA file		contigs.fa : contig FASTA file

			<pre style="background:yellow">
	Contigs stats:		Contigs stats:
	#elem min max mean median n50 sum		#elem min max mean median n50 sum
Line 807:		Line 808:
	breaks(200+) 251 (-b 20) coming from 170 ctgs		breaks(200+) 251 (-b 20) coming from 170 ctgs
	1,273,164 singletons; 879,840 of them aligned by soap (-v5,-s12,-g3) to PA14		1,273,164 singletons; 879,840 of them aligned by soap (-v5,-s12,-g3) to PA14
			</pre>

	Distance between breakpoints:		Distance between breakpoints:

2010-10-12T20:01:27Z

CBCB

← Older revision		Revision as of 20:01, 12 October 2010
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	=== CBCB ===		=== CBCB ===

			<pre style="background:yellow">
	Data: 33 bp Solexa reads from 2 libraries		Data: 33 bp Solexa reads from 2 libraries
	lib #reads #reads(1+N's) #reads(2+N's)		lib #reads #reads(1+N's) #reads(2+N's)
Line 11:		Line 12:
	total 8,627,900		total 8,627,900
	~ 43.55X cvg		~ 43.55X cvg
			</pre>

	Files:		Files:

2010-10-05T18:03:19Z

NCBI

← Older revision		Revision as of 18:03, 5 October 2010
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	Ranging from 6.2M to 6.9M		Ranging from 6.2M to 6.9M
	PA14 CP000438 6,537,648 bp, 66.29 %GC : 5,892 genes most similar to PAb1		PA14 CP000438 6,537,648 bp, 66.29 %GC : 5,892 protein coding genes most similar to PAb1
	PAO1 AE004091 6,264,404 bp, 66.56 %GC : 5,568 genes rearrangement vs PA14		PAO1 AE004091 6,264,404 bp, 66.56 %GC : 5,568 genes rearrangement vs PA14
	PACS2 AAQW01000001.1 6,492,423 bp, 66.33% GC : 5,676 genes rearrangement vs PA14		PACS2 AAQW01000001.1 6,492,423 bp, 66.33% GC : 5,676 genes rearrangement vs PA14
	PA2192 . 6,905,121 bp, 65.99% GC : 6,157 genes rearrangement vs PA14		PA2192 . 6,905,121 bp, 65.99% GC : 6,157 genes rearrangement vs PA14
	PAC3719 . 6,222,097 bp, 66.30% GC : 5,650 genes no rearrangement vs PA14		PAC3719 . 6,222,097 bp, 66.30% GC : 5,650 genes no rearrangement vs PA14
	PA7 CP000744 6,588,339 bp : 6,286 genes no rearrangement vs PA14		PA7 CP000744 6,588,339 bp : 6,286 genes no rearrangement vs PA14
	PALESB58 FM209186 6,601,757 bp 66% GC (new)		PALESB58 FM209186 6,601,757 bp 66% GC : 5,925 (new)

2010-10-05T17:57:25Z

NCBI

← Older revision		Revision as of 17:57, 5 October 2010
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	PAC3719 . 6,222,097 bp, 66.30% GC : 5,650 genes no rearrangement vs PA14		PAC3719 . 6,222,097 bp, 66.30% GC : 5,650 genes no rearrangement vs PA14
	PA7 CP000744 6,588,339 bp : 6,286 genes no rearrangement vs PA14		PA7 CP000744 6,588,339 bp : 6,286 genes no rearrangement vs PA14
			PALESB58 FM209186 6,601,757 bp 66% GC (new)


	All vs all nucmer alignments:		All vs all nucmer alignments:

2010-10-05T17:47:02Z

NCBI

← Older revision		Revision as of 17:47, 5 October 2010
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	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas Pseudomonas genome projects]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas Pseudomonas genome projects]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas%20aeruginosa Pseudomonas aeruginosa genome projects]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas%20aeruginosa Pseudomonas aeruginosa genome projects]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Link&LinkName=genomeprj_sra&from_uid=28809 PAb1 SRA (~~data not~~ uploaded)]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Link&LinkName=genomeprj_sra&from_uid=28809 PAb1 SRA (uploaded)]

	'''Same Strains'''		'''Same Strains'''

2010-10-05T17:33:40Z

Data

← Older revision		Revision as of 17:33, 5 October 2010
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	s_7 4,521,907 69,669 59,589		s_7 4,521,907 69,669 59,589
	total 8,627,900		total 8,627,900
			~ 43.55X cvg

	~~~ 43.55X cvg~~

	~~File location:~~
	~~/fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/~~

	Files:		Files:
	s_1_sequence.txt # contains seq & qual; seq names: HWI% ; all reads are 33 bp		s_1_sequence.txt # contains seq & qual; seq names: HWI% ; all reads are 33 bp
Line 34:		Line 30:
	s_1 135497769 1863585 3231899 -5 28.2624918053079 40 3829504586		s_1 135497769 1863585 3231899 -5 28.2624918053079 40 3829504586
	s_7 149222931 1357384 3113806 -5 31.0508663175903 40 4633501282		s_7 149222931 1357384 3113806 -5 31.0508663175903 40 4633501282

			/fs/szasmg2/Bacteria/Pseudomonas_aeruginosa/

	=== NCBI ===		=== NCBI ===

2010-10-05T17:32:53Z

Data

← Older revision		Revision as of 17:32, 5 October 2010
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	=== CBCB ===		=== CBCB ===

	~~Reads~~:		Data: 33 bp Solexa reads from 2 libraries
	~~8627900~~ 33 bp Solexa reads		lib #reads #reads(1+N's) #reads(2+N's)
			s_1 4,105,993 37,933 18,771
			s_7 4,521,907 69,669 59,589
			total 8,627,900

	~~Coverage:~~ ~ 43.55X		~ 43.55X cvg

	File location:		File location:
Line 22:		Line 25:
	s_7_tag.txt		s_7_tag.txt

	~~wc -l s_1_sequence.txt s_7_sequence.txt~~
	~~4105993 s_1_sequence.txt~~
	~~4521907 s_7_sequence.txt~~
	~~8627900 total~~

	~~#all reads that contain at least 1 ambiguity~~
	~~grep -c N s_*seq~~
	~~s_1_sequence.seq:37933~~
	~~s_7_sequence.seq:69669~~

	~~#all reads that contain at least 2 ambiguities~~
	~~cat s_1_sequence.seq \| perl -ane 'print $_ if(/N.+N/);' \| wc -l : 18771~~
	~~cat s_7_sequence.seq \| perl -ane 'print $_ if(/N.+N/);' \| wc -l : 59589~~
	~~...~~

	s_1 reads have significantly fewer N's than s_7 reads !!!		s_1 reads have significantly fewer N's than s_7 reads !!!
	s_1 reads align better to ref than s_2 reads !!!		s_1 reads align better to ref than s_2 reads !!!

2009-09-21T15:45:11Z

NCBI

← Older revision		Revision as of 15:45, 21 September 2009
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	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas Pseudomonas genome projects]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas Pseudomonas genome projects]
	* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas%20aeruginosa Pseudomonas aeruginosa genome projects]		* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=search&term=Pseudomonas%20aeruginosa Pseudomonas aeruginosa genome projects]
			* [http://www.ncbi.nlm.nih.gov/sites/entrez?db=genomeprj&cmd=Link&LinkName=genomeprj_sra&from_uid=28809 PAb1 SRA (data not uploaded)]

	'''Same Strains'''		'''Same Strains'''