Daniel:Notebook/GenomeMiner/2013-10-9: Difference between revisions
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'''Novoalign''' | '''Novoalign''' | ||
novoalign -d index_v4s3fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s3.sam | novoalign -d index_v4s3fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s3.sam | ||
===Alignment Results=== | |||
# Read Sequences: 11450664 | |||
# Aligned: 4180484 | |||
# Unique Alignment: 4172662 | |||
# Gapped Alignment: 2905583 | |||
# Quality Filter: 25772 | |||
# Homopolymer Filter: 38 | |||
# Elapsed Time: 10011.583 (sec.) | |||
# CPU Time: 128.9 (min.) | |||
# Done at Wed Oct 9 13:18:23 2013 | |||
===Error Counting Results=== | |||
Error Rate: 6.73% | |||
Error Rate of Insertions: 3.26% | |||
Error Rate of Deletions: 2.35% | |||
Error Rate of Substitutions: 1.12% |
Latest revision as of 05:28, 10 October 2013
HL155 Novoalign (Started 10/3/2013)[edit]
V4S3[edit]
Pipeline[edit]
Build Index
novoindex index_v4s3fullrevcomp.ndx V4S3_fullrevcomp.fa
Novoalign
novoalign -d index_v4s3fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s3.sam
Alignment Results[edit]
# Read Sequences: 11450664 # Aligned: 4180484 # Unique Alignment: 4172662 # Gapped Alignment: 2905583 # Quality Filter: 25772 # Homopolymer Filter: 38 # Elapsed Time: 10011.583 (sec.) # CPU Time: 128.9 (min.) # Done at Wed Oct 9 13:18:23 2013
Error Counting Results[edit]
Error Rate: 6.73% Error Rate of Insertions: 3.26% Error Rate of Deletions: 2.35% Error Rate of Substitutions: 1.12%