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lecture_notes:05-27-2011 [2011/05/27 21:35] eyliaw |
lecture_notes:05-27-2011 [2011/05/27 22:18] eyliaw |
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* Try mapping with Newbler or BWA. | * Try mapping with Newbler or BWA. | ||
* BLAST/BLAT it. | * BLAST/BLAT it. | ||
+ | * Find insert lengths for the SeqPrep + Quake corrected Illumina data. | ||
* SOAPdenovo assembly try 1: | * SOAPdenovo assembly try 1: | ||
- | * Only on Illumina data | + | * Only on Illumina data. |
* try 2: | * try 2: | ||
- | * Level 1: All Illumina data for contig building. | + | * Rank 1: All Illumina data for contig building. |
- | * Level 2: 454 data for scaffolding. | + | * Rank 2: 454 data for scaffolding. |
- | * Find insert lengths for the Quake corrected Illumina data. | + | * try 3: |
+ | * Illumina + 454 data as rank 1. | ||
+ | * # If insert length is negative, don't treat them as PE reads. | ||
+ | * Newbler run. | ||
+ | * Take another look at Barcode of Life mapping: [[http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG5|Invertebrate mitochondrial translation table]] | ||
+ | * |