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lecture_notes:05-27-2011 [2011/05/27 21:24] eyliaw |
lecture_notes:05-27-2011 [2011/05/28 03:29] karplus fixed mistake on meaning of "rank 2". added info about barcode of life. |
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====== To Do ====== | ====== To Do ====== | ||
- | We went over some things that need updating in the wiki. | + | We went over some things that need updating in the wiki and plans for this weekend. |
* Document scripts added in [[computer_resources:bin|bin]] folder. | * Document scripts added in [[computer_resources:bin|bin]] folder. | ||
- | * Find out which lanes in 454 run 3 are banana slug runs. | + | |
+ | |||
+ | * Find out which lanes in 454 run 3 are banana slug runs. But it turns out that this is not necessary: run "3" is not a separate run, but just run2 plus the non-banana-slug reads in other lanes. | ||
* Try mapping with Newbler or BWA. | * Try mapping with Newbler or BWA. | ||
* BLAST/BLAT it. | * BLAST/BLAT it. | ||
- | * SOAPdenovo assembly: | + | * Find insert lengths for the SeqPrep + Quake corrected Illumina data. |
- | * Level 1: Illumina data for contig building. | + | * SOAPdenovo assembly try 1: |
- | * Level 2: 454 data for scaffolding. | + | * Only on Illumina data. |
+ | * try 2: | ||
+ | * Rank 1: All Illumina data as rank 1. | ||
+ | * Rank 2: 454 data as rank 2 (both for contig building and scaffolding). | ||
+ | * try 3: | ||
+ | * Illumina + 454 data as rank 1. | ||
+ | * # If insert length is negative, don't treat them as PE reads. | ||
+ | * Newbler assemblies—no need for a new one, as there is no new 454 data. | ||
+ | * Take another look at Barcode of Life mapping: [[http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG5|Invertebrate mitochondrial translation table]] | ||
+ | * It turns out that blastall does not seem to have any documented way to tell tblastx to use a different genetic code, though the NCBI web server has the option. | ||
+ | * The work Kevin did so far is now in assemblies/slug/barcode-of-life. | ||
+ | * Next step is to use BWA to find all the SeqPrep+Quake treated Illumina reads that map to what has been found so far of the barcode. | ||
+ | |||
+ | |||
+ | * Ed presenting paper on Wednesday. Get paper over the weekend. |