Transcriptomics-Tobacco - Revision history

Raj at 10:24, 5 July 2013

2013-07-05T10:24:38Z

2013-07-05T10:24:15Z

← Older revision		Revision as of 10:24, 5 July 2013
Line 14:		Line 14:
	** Get the final list of genes characterized : JAN 2011		** Get the final list of genes characterized : JAN 2011
	** '''Manuscript''' MAR 2011		** '''Manuscript''' MAR 2011

	=Scientific Assumptions=		=Scientific Assumptions=

	=Strategy=		=Strategy=
	* Gene Prediction		* Gene Prediction
Line 29:		Line 27:
	** Use the contrasting samples to hybridise them to assign gene status and differentially expressed		** Use the contrasting samples to hybridise them to assign gene status and differentially expressed
	* Validate the identified genes		* Validate the identified genes

	=Data=		=Data=
	* TGI downloaded Sequences		* TGI downloaded Sequences
Line 39:		Line 36:
	* TOBEA		* TOBEA
	** EST contigs: '''40642'''		** EST contigs: '''40642'''

	=Implementation=		=Implementation=
	=== Mapping ESTs on Genomics DNA ===		=== Mapping ESTs on Genomics DNA ===
Line 64:		Line 60:
	** Total number of TOBEA-ESTs:		** Total number of TOBEA-ESTs:
	** Total number of Unigenes:		** Total number of Unigenes:

	=== Gene prediction if TGI contig===		=== Gene prediction if TGI contig===
	** Genome threading		** Genome threading

2010-06-04T07:34:28Z

← Older revision		Revision as of 07:34, 4 June 2010
Line 2:		Line 2:
	* Get the differentially expressed Genes in tobacco leaf		* Get the differentially expressed Genes in tobacco leaf
	* Author: Guru and Rajkumar and et al		* Author: Guru and Rajkumar and et al
	* ~~Timeline~~		* Time line
	** Sequencing of ESTs: SEP 2009		** Sequencing of ESTs: SEP 2009
	** Assemble / pre annotation: NOV 2009		** Assemble / pre annotation: NOV 2009
	** Printing Array : JAN 2010		** Printing Array : JAN 2010
	** Combining the protein data: MAR 2010		** Combining the protein data: MAR 2010
	** Re annotation of ~~hybridised~~ '''genes''' : APR 2010		** Re annotation of hybridized '''genes''' : APR 2010
	** ~~Consenses~~ of the 2 data for the selected genes (MAY 2010)		** Con senses of the 2 data for the selected genes (MAY 2010)
	** Validate selected genes (100) by RT: JUN 2010		** Validate selected genes (100) by RT: JUN 2010
	** '''Manuscript''' (after approval from ITC): JUL 2010		** '''Manuscript''' (after approval from ITC): JUL 2010
	** Lab validation of selected genes: DEC 2010		** Lab validation of selected genes: DEC 2010
	** Get the final list of genes ~~characterised~~ : JAN 2011		** Get the final list of genes characterized : JAN 2011
	** '''Manuscript''' MAR 2011		** '''Manuscript''' MAR 2011

2010-06-03T11:29:02Z

Mapping ESTs on Genomics DNA

← Older revision		Revision as of 11:29, 3 June 2010
Line 60:		Line 60:
	** [[GTH_EST-gDNA]] \| 3 days		** [[GTH_EST-gDNA]] \| 3 days
	* Results		* Results
			** [[count_fasta.pl]] \| Counting the frequency
	** Total number of ITC-ESTs:		** Total number of ITC-ESTs:
	** Total number of TOBEA-ESTs:		** Total number of TOBEA-ESTs:

2010-06-01T09:09:27Z

Mapping ESTs on Genomics DNA

← Older revision		Revision as of 09:09, 1 June 2010
Line 59:		Line 59:
	** [[parse assemblage ITC_EST-TOBEA_EST]] \| 3 sec		** [[parse assemblage ITC_EST-TOBEA_EST]] \| 3 sec
	** [[GTH_EST-gDNA]] \| 3 days		** [[GTH_EST-gDNA]] \| 3 days
			* Results
			** Total number of ITC-ESTs:
			** Total number of TOBEA-ESTs:
			** Total number of Unigenes:

	=== Gene prediction if TGI contig===		=== Gene prediction if TGI contig===

2010-06-01T08:44:39Z

Mapping ESTs on Genomics DNA

← Older revision		Revision as of 08:44, 1 June 2010
Line 58:		Line 58:
	** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used		** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used
	** [[parse assemblage ITC_EST-TOBEA_EST]] \| 3 sec		** [[parse assemblage ITC_EST-TOBEA_EST]] \| 3 sec
	** [[GTH_EST-gDNA]]		** [[GTH_EST-gDNA]] \| 3 days

	=== Gene prediction if TGI contig===		=== Gene prediction if TGI contig===

2010-05-08T02:48:02Z

Mapping ESTs on Genomics DNA

← Older revision		Revision as of 02:48, 8 May 2010
Line 57:		Line 57:
	** [[rename ESTs]] \| 5 min		** [[rename ESTs]] \| 5 min
	** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used		** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used
	** [[parse assemblage ITC_EST-TOBEA_EST]]		** [[parse assemblage ITC_EST-TOBEA_EST]] \| 3 sec
	** [[GTH_EST-gDNA]]		** [[GTH_EST-gDNA]]

2010-05-07T16:41:40Z

Mapping ESTs on Genomics DNA

← Older revision		Revision as of 16:41, 7 May 2010
Line 55:		Line 55:
	** [[rename BACs]] \| few sec		** [[rename BACs]] \| few sec
	** [[rename TGI]] \| 12 min		** [[rename TGI]] \| 12 min
	** [[rename ESTs]] \|		** [[rename ESTs]] \| 5 min
	** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used		** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used
	** [[parse assemblage ITC_EST-TOBEA_EST]]		** [[parse assemblage ITC_EST-TOBEA_EST]]

2010-05-07T16:40:18Z

Mapping ESTs on Genomics DNA

← Older revision		Revision as of 16:40, 7 May 2010
Line 55:		Line 55:
	** [[rename BACs]] \| few sec		** [[rename BACs]] \| few sec
	** [[rename TGI]] \| 12 min		** [[rename TGI]] \| 12 min
			** [[rename ESTs]] \|
	** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used		** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used
	** [[parse assemblage ITC_EST-TOBEA_EST]]		** [[parse assemblage ITC_EST-TOBEA_EST]]

2010-05-01T07:16:34Z

Mapping ESTs on Genomics DNA

← Older revision		Revision as of 07:16, 1 May 2010
Line 44:		Line 44:
	:Impractical because tgi_singlet vs est_contig -> >8 days of continuous run in quad core machine		:Impractical because tgi_singlet vs est_contig -> >8 days of continuous run in quad core machine
	* Strategy		* Strategy
	** Assembling TOBEA EST and ITC-EST (~80,000 sequences) \| Merge singlet and contigs and name it.		** EST
	** Merge TGI contig and TGI singlet (6.5 lakhs sequences) \| name individual fasta		*** Assembling TOBEA EST and ITC-EST (~80,000 sequences) \| Merge singlet and contigs and name it.
	** Merge All Bacs and name individual fasta		** Genomic DNA
	** Merge all genomic DNA		*** Merge TGI contig and TGI singlet (6.5 lakhs sequences) \| name individual fasta
	** GT on ~~EST vs~~ gDNA		*** Merge All Bacs and name individual fasta
			*** Merge all genomic DNA
			** Mapping (Genome Threader) EST on gDNA
	* Pipes		* Pipes
	** [[uncompress BACs]] \| few sec		** [[uncompress BACs]] \| few sec

← Older revision		Revision as of 16:41, 7 May 2010
Line 55:		Line 55:
	** [[rename BACs]] \| few sec		** [[rename BACs]] \| few sec
	** [[rename TGI]] \| 12 min		** [[rename TGI]] \| 12 min
	** [[rename ESTs]] \|		** [[rename ESTs]] \| 5 min
	** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used		** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used
	** [[parse assemblage ITC_EST-TOBEA_EST]]		** [[parse assemblage ITC_EST-TOBEA_EST]]

← Older revision		Revision as of 16:40, 7 May 2010
Line 55:		Line 55:
	** [[rename BACs]] \| few sec		** [[rename BACs]] \| few sec
	** [[rename TGI]] \| 12 min		** [[rename TGI]] \| 12 min
			** [[rename ESTs]] \|
	** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used		** [[assemble ITC_EST-TOBEA_EST]] \| 26min \| 16core implementation, but after 3 min only one core was used
	** [[parse assemblage ITC_EST-TOBEA_EST]]		** [[parse assemblage ITC_EST-TOBEA_EST]]