Transcriptomics-Tobacco: Difference between revisions
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=Implementation= | =Implementation= | ||
=== Mapping ESTs on Genomics DNA === | === Mapping ESTs on Genomics DNA === | ||
:Impractical because tgi_singlet vs est_contig -> >8 days of continuous run in | :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 | ** Assembling TOBEA EST and ITC-EST (~80,000 sequences) | Merge singlet and contigs and name it. | ||
** Merge TGI contig and TGI singlet (6.5 lakhs sequences) | name individual fasta | ** Merge TGI contig and TGI singlet (6.5 lakhs sequences) | name individual fasta | ||
** Merge All Bacs and name individual fasta | ** Merge All Bacs and name individual fasta | ||
| Line 52: | Line 52: | ||
** [[uncompress BACs]] | ** [[uncompress BACs]] | ||
** [[rename BACs]] | ** [[rename BACs]] | ||
** [[rename TGI]] | |||
** [[assemble ITC_EST-TOBEA_EST]] | |||
** [[GTH_EST-gDNA]] | |||
=== Gene prediction if TGI contig=== | === Gene prediction if TGI contig=== | ||
Revision as of 13:21, 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 Genomics DNA
- Impractical because tgi_singlet vs est_contig -> >8 days of continuous run in quad core machine
- Strategy
- Assembling TOBEA EST and ITC-EST (~80,000 sequences) | Merge singlet 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
- Pipes
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