Daniel:Notebook/GenomeMiner/2013-10-10
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HL155 Novoalign (Started 10/3/2013)
V4S1 (no FULLNW)
The fullnw tag on novoalign tries to align the entire read to the entire reference, a good option when we were using the shortened references, but on the full references it might cause issues (recall high error rates from Mon,Tues, and Wed.
Pipeline
Made a modified bash script to do everything for me. Bash script:
Alignment Results
# Read Sequences: 11450664 # Aligned: 4194879 # Unique Alignment: 4178621 # Gapped Alignment: 3042944 # Quality Filter: 23301 # Homopolymer Filter: 40 # Elapsed Time: 9952.305 (sec.) # CPU Time: 140.8 (min.)