Transcriptomics-Tobacco: Difference between revisions
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*** Impractical because tgi_singlet vs est_contig -> >8 days of continuous run in quadcore machine | *** Impractical because tgi_singlet vs est_contig -> >8 days of continuous run in quadcore machine | ||
*** Impractical because tgi_singlet vs est_singlet ->> month of continuous run in quadcore machine | *** Impractical because tgi_singlet vs est_singlet ->> month of continuous run in quadcore machine | ||
** New machine | |||
*** Assembling TOBEA EST and ITC-EST (~80,000 sequences) | Merge siglet and contigs and name it. | |||
*** Merge TGI contig and TGI singlet (6.5 lakhs sequences) | name individual fasta | |||
*** Merge All Bacs and name individual fasta | |||
*** Merge all genomic DNA | |||
*** GT on EST vs gDNA | |||
* Gene prediction if TGI contig | * Gene prediction if TGI contig | ||
** Genome threading | ** Genome threading | ||
| Line 50: | Line 56: | ||
*** Multithreaded | *** Multithreaded | ||
* Comparing Unique TOBEA EST contigs | * Comparing Unique TOBEA EST contigs | ||
** Tobea ESTs are from all the tissues, while our Tobacco ESTs are from Leaf. | ** Tobea ESTs are from all the tissues, while our Tobacco ESTs are from Leaf. Getting the unique TOBEA EST will help to add to the present array | ||
** Process | ** Process | ||
** Script | ** Script | ||
*** [[blast_tobea]] | *** [[blast_tobea]] | ||
*** [[parse_tobea]] | *** [[parse_tobea]] | ||
* Some Tools | * Some Tools | ||
** [[gth_run]] | ** [[gth_run]] | ||
** [[trim_seq]] | Filter "N", size | ** [[trim_seq]] | Filter "N", size | ||
** [[multifasta-fastas]] | ** [[multifasta-fastas]] | ||
Revision as of 10:39, 28 April 2010
Tobacco Pipeline Target
- Get the differentially expressed Genes in tobacco leaf
- Author: Guru and Rajkumar and et al
- Timeline
- Sequencing of ESTs: SEP 2009
- Assemble / pre annotation: NOV 2009
- Printing Array : JAN 2010
- Combining the protein data: MAR 2010
- Re annotation of hybridised genes : APR 2010
- Consenses of the 2 data for the selected genes (MAY 2010)
- Validate selected genes (100) by RT: JUN 2010
- Manuscript (after approval from ITC): JUL 2010
- Lab validation of selected genes: DEC 2010
- Get the final list of genes characterised : JAN 2011
- Manuscript MAR 2011
Scientific Assumptions
Strategy
- Gene Prediction
- Flavour +/- tobacco samples
- Extract mRNA and made ESTs
- Sequencing and EST short reads
- Assemble the EST reads (contigs and singlets)
- Annotated the contigs
- Meaningful EST pieces
- Implanted them on micro array
- Further annotate them to spot reliable genes to the existing models
- Use the contrasting samples to hybridise them to assign gene status and differentially expressed
- Validate the identified genes
Data
- TGI downloaded Sequences
- tgi_contig : 81,959
- tgi_singlet: 5,58,987
- EST Unigene assembled
- est_contig: 38,261
- est_singlet: ~2 lakh (damaged)
- TOBEA
- EST contigs: 40642
Implementation
- Mapping ESTs on tgi
- Genome threading or Blat
- Impractical because tgi_singlet vs est_contig -> >8 days of continuous run in quadcore machine
- Impractical because tgi_singlet vs est_singlet ->> month of continuous run in quadcore machine
- New machine
- Assembling TOBEA EST and ITC-EST (~80,000 sequences) | Merge siglet and contigs and name it.
- Merge TGI contig and TGI singlet (6.5 lakhs sequences) | name individual fasta
- Merge All Bacs and name individual fasta
- Merge all genomic DNA
- GT on EST vs gDNA
- Genome threading or Blat
- Gene prediction if TGI contig
- Genome threading
- TGI_CONTIG vs EST_CONTIG
- Multithreaded
- Genome threading
- Comparing Unique TOBEA EST contigs
- Tobea ESTs are from all the tissues, while our Tobacco ESTs are from Leaf. Getting the unique TOBEA EST will help to add to the present array
- Process
- Script
- Some Tools
- gth_run
- trim_seq | Filter "N", size
- multifasta-fastas