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lecture_notes:04-18-2011

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lecture_notes:04-18-2011 [2011/04/18 23:33]
eyliaw
lecture_notes:04-18-2011 [2015/07/28 08:12]
149.155.218.110 ↷ Links adapted because of a move operation
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-====== Game plan ====== +====== Game Plan ====== 
-Today, ​Kevin outlined the steps we should take to evaluate the data we have now.  We currently have 454 contigs built with [[bioinformatic_tools:​gs_de_novo_assembler|Newbler]] (but with a high error rate, so likely repeat regions were being joined). ​ The 454 data has poor coverage as well, but may work well as a starting point for [[bioinformatic_tools:​price|PRICE]],​ using Illumina data to extend them.+Kevin outlined the steps we should take to evaluate the data we have now.  We currently have 454 contigs built with [[archive:bioinformatic_tools:​gs_de_novo_assembler|Newbler]] (but with a high error rate, so likely repeat regions were being joined). ​ The 454 data has poor coverage as well, but may work well as a starting point for [[archive:bioinformatic_tools:​price|PRICE]],​ using Illumina data to extend them.
  
 So, our next steps are to: So, our next steps are to:
-  - Count kmers in Illumina data with [[bioinformatic_tools:​jellyfish|Jellyfish]] +  - Count kmers in Illumina data with [[archive:bioinformatic_tools:​jellyfish|Jellyfish]] 
-  - Filter kmers with [[bioinformatic_tools:​quake|Quake]] +  - Filter kmers with [[archive:bioinformatic_tools:​quake|Quake]] 
-  - Trim with [[bioinformatic_tools:​seqprep|SeqPrep]] +  - Trim with [[archive:bioinformatic_tools:​seqprep|SeqPrep]] 
-  - Rebuild 454 contigs with [[bioinformatic_tools:​gs_de_novo_assembler|Newbler]] 2.5.3+  - Rebuild 454 contigs with [[archive:bioinformatic_tools:​gs_de_novo_assembler|Newbler]] 2.5.3
   - Initialize PRICE with 454 contigs and extend with trimmed and filtered Illumina reads   - Initialize PRICE with 454 contigs and extend with trimmed and filtered Illumina reads
lecture_notes/04-18-2011.txt · Last modified: 2015/07/28 08:12 by 149.155.218.110