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lecture_notes:04-18-2011 [2011/04/19 03:52] eyliaw created |
lecture_notes:04-18-2011 [2015/07/28 15:12] (current) 149.155.218.110 ↷ Links adapted because of a move operation |
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- | ====== Gameplan ====== | + | ====== 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 |