Casuarina SSR: Difference between revisions
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===Develop unigenes=== | ===Develop unigenes=== | ||
* TGICL is used | * TGICL is used | ||
* Contigs : | ** Param: | ||
* Singlets: | <pre> | ||
# -l miminum overlap length (default 40) | |||
# -M ignore lower-case masking in <fasta_db> sequences | |||
# -p minimum percent identity for overlaps <PID> (default 94) | |||
</pre> | |||
* Contigs : '''3947''' | |||
* Singlets: '''475''' | |||
===Generate statistics=== | ===Generate statistics=== | ||
Revision as of 04:00, 29 December 2011
New SSRs Pipeline Target
- Designing Cross species EST SSRs from Casuarina
- Author: Ashok Kulkarni and Rajkumar
- Timeline
- Designing Primers: DEC 2011
- Oligo synthesis : JAN 2012
- Standardisation and Validation : MAR 2010
- Manuscript : JUN 2010
Scientific Assumptions
EST SSRs are supposedly conserved across species therefore higher species transferability is expected
Strategy
- C. glauca ESTs
- Develop unigenes
- Generate statistics
- Filter the sequence
- Mine for repeat motifs
- Design Primers
Implementation
C. glauca ESTs
- Total Number of ESTs: 34897
- Total number of C. glauca ESTs: 34805
Develop unigenes
- TGICL is used
- Param:
# -l miminum overlap length (default 40) # -M ignore lower-case masking in <fasta_db> sequences # -p minimum percent identity for overlaps <PID> (default 94)
- Contigs : 3947
- Singlets: 475
Generate statistics
- Distribution of length in contigs:
- Distribution of length in singlets:
- Final number of sequence
- Param: Trimmed off the <220bp | Trimmed off the N>5%
- ID Named