Daniel:Notebook/GenomeMiner/2013-10-10

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Revision as of 20:47, 10 October 2013 by >Djacobse (Created page with "=HL155 Novoalign (Started 10/3/2013)= Back to Calendar ==V4S1 (no FULLNW)== The fullnw tag on novo...")
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HL155 Novoalign (Started 10/3/2013)

Back to Calendar

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.)