Difference between revisions of "Project Priority List"
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− | + | ==Genome Assembly== | |
*Website modules that take in parameters and have a tutorial (probably want a few frames in webpage that can load individually) | *Website modules that take in parameters and have a tutorial (probably want a few frames in webpage that can load individually) | ||
**At the end with the contig you compare them and also discuss the next steps of scaffolding (be sure to highlight the importance of having linker sequences) | **At the end with the contig you compare them and also discuss the next steps of scaffolding (be sure to highlight the importance of having linker sequences) | ||
+ | **Have a pre and post test to evaluate program | ||
− | #Make the website to show changes in assembly based on changes in... | + | #Make the website to show changes in assembly based on changes in... - include pre analysis of raw reads with the scripts I have already made |
#*kmer length | #*kmer length | ||
− | #*Lower coverage... using 1/2 reads | + | #*Lower coverage... using 1/2 reads. Or using have a % of the reads to use |
+ | #*Combine multiple reads from organisms and see if can pull out individual genomes | ||
#*Not cleaning reads | #*Not cleaning reads | ||
#Tutorial - include walkthrough and explain scaffolding as well | #Tutorial - include walkthrough and explain scaffolding as well | ||
Line 16: | Line 18: | ||
#Scaffolding addition to website | #Scaffolding addition to website | ||
− | ===Phages DB (2nd priority) | + | ===Timeline Plan=== |
+ | #Finish maximum likelihood fitting of gaussian distribution (1.5 days max... if not done then, move on and come back to this later) | ||
+ | #Choose assembly program. Considerations: | ||
+ | #*OLC or de Bruijn? | ||
+ | #*Can it run on the GCAT webserver? | ||
+ | #*What is the pipeline from contig to scaffold? | ||
+ | #*What kind of genome to use to develop parameters | ||
+ | #Make forms and version of assembly program online... link of all of the forms and options | ||
+ | #Work on tutorial text... begin with outline and fill in (I will also be taking notes for this section throughout the summer). | ||
+ | #*Throughout this process take notes of figure ideas or animations | ||
+ | #*STORYBOARD | ||
+ | #Bring the web assembly pipeline and tutorial tool together in website... Considerations: | ||
+ | #*Easy to add to - like adding more modules (different assembly methods, genome comparisons, figures...) | ||
+ | #*Organized and easy to follow | ||
+ | #Investigate genome comparison tools | ||
+ | #*Either locate one to implement on web or create one | ||
+ | #Add this to existing website | ||
+ | |||
+ | ==Phages DB (2nd priority)== | ||
*Take 2 groups of phages and pull out patterns | *Take 2 groups of phages and pull out patterns | ||
**x % in group has 1 mobile element... | **x % in group has 1 mobile element... | ||
*Query based comparison | *Query based comparison | ||
**Give me gene X, and return list of gene and what % in one cluster... ect. | **Give me gene X, and return list of gene and what % in one cluster... ect. |
Latest revision as of 15:43, 15 June 2011
Genome Assembly
- Website modules that take in parameters and have a tutorial (probably want a few frames in webpage that can load individually)
- At the end with the contig you compare them and also discuss the next steps of scaffolding (be sure to highlight the importance of having linker sequences)
- Have a pre and post test to evaluate program
- Make the website to show changes in assembly based on changes in... - include pre analysis of raw reads with the scripts I have already made
- kmer length
- Lower coverage... using 1/2 reads. Or using have a % of the reads to use
- Combine multiple reads from organisms and see if can pull out individual genomes
- Not cleaning reads
- Tutorial - include walkthrough and explain scaffolding as well
- Words/actual text
- Graphics - maybe make interactive graphics with html 5 technology... adobe flex, processing.js
- Animations
- Genome comparison
- dotplot to visually compare contigs - program automatically rearranges all contigs of one to get as close to diagonal line as possible
- Effect of OLC vs de Bruijn - too technical?
- Scaffolding addition to website
Timeline Plan
- Finish maximum likelihood fitting of gaussian distribution (1.5 days max... if not done then, move on and come back to this later)
- Choose assembly program. Considerations:
- OLC or de Bruijn?
- Can it run on the GCAT webserver?
- What is the pipeline from contig to scaffold?
- What kind of genome to use to develop parameters
- Make forms and version of assembly program online... link of all of the forms and options
- Work on tutorial text... begin with outline and fill in (I will also be taking notes for this section throughout the summer).
- Throughout this process take notes of figure ideas or animations
- STORYBOARD
- Bring the web assembly pipeline and tutorial tool together in website... Considerations:
- Easy to add to - like adding more modules (different assembly methods, genome comparisons, figures...)
- Organized and easy to follow
- Investigate genome comparison tools
- Either locate one to implement on web or create one
- Add this to existing website
Phages DB (2nd priority)
- Take 2 groups of phages and pull out patterns
- x % in group has 1 mobile element...
- Query based comparison
- Give me gene X, and return list of gene and what % in one cluster... ect.