lecture_notes:05-15-2015
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lecture_notes:05-15-2015 [2015/05/18 15:01] gepoliano |
lecture_notes:05-15-2015 [2015/05/18 15:11] (current) gepoliano |
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| =====SGA update===== | =====SGA update===== | ||
| - | -SGA is a memory efficient assembler | + | * SGA is a memory efficient assembler |
| - | -It was possible to compute more compressed data | + | * It was possible to compute more compressed data |
| - | -The pipeline changed, since it was not easy to figure out how to run it | + | * The pipeline changed, since it was not easy to figure out how to run it |
| - | -It was necessary to make sure the parameters are running | + | * It was necessary to make sure the parameters are running |
| - | -The group assembled one dataset, merged together | + | * The group assembled one dataset, merged together |
| - | -SGA indexed each dataset separated | + | * SGA indexed each dataset separated |
| - | -Merging is complicated in a pairwise fashion, then two pairs were merged at a time | + | * Merging is complicated in a pairwise fashion, then two pairs were merged at a time |
| - | -Indexing all three sistinct submissions | + | * Indexing all three sistinct submissions |
| - | -Pre-processed adapter trimming | + | * Pre-processed adapter trimming |
| - | -Duplicate-removal is later than indexing | + | * Duplicate-removal is later than indexing |
| - | -One issue the group found: SW018 and 19, same library are optical PCR duplicates that should be removed | + | * One issue the group found: SW018 and 19, same library are optical PCR duplicates that should be removed |
| + | * The overall duplication level is a problem | ||
| + | * Each datset was generated independently | ||
| + | * Then, removing duplicates should be done apart for each dataset | ||
| + | * The dataset is very complicated - there is big duplication rate across the dataset the group has | ||
| + | * Merging indexes - planning on pulling some stats from the grin engine to pull information | ||
| + | * The wall time is large | ||
| + | * A variant file with the bubble pop counted the contigs | ||
| + | * The group is planning on using the mate-pair data | ||
| + | * Do adapter removal and index removal - using skewer | ||
| + | * | ||
lecture_notes/05-15-2015.1431961305.txt.gz · Last modified: 2015/05/18 15:01 by gepoliano
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