Daniel:Notebook/GenomeMiner/2013-10-15: Difference between revisions
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==V4S1 Novoalign (Changing Index Length)== | ==V4S1 Novoalign (Changing Index Length)== | ||
Attempting to fix these issues with Novoalign by changing the k-mer length when creating the index. | |||
===Pipeline=== | |||
novoindex -k 98 index_V4S1_fullrevcomp.ndx V4S1_fullrevcomp.fa | |||
novoalign -d index_V4S1_fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM > v4s1_novo.sam | |||
the rest of the [[bash script | |||
===Alignment Results=== | ===Alignment Results=== |
Revision as of 00:27, 16 October 2013
HL155 Novoalign (Started 10/3/2013)
V4S1 Novoalign (Changing Index Length)
Attempting to fix these issues with Novoalign by changing the k-mer length when creating the index.
Pipeline
novoindex -k 98 index_V4S1_fullrevcomp.ndx V4S1_fullrevcomp.fa novoalign -d index_V4S1_fullrevcomp.ndx -f ../../s_2_1_Indx13.txt -F ILMFQ -r ALL -o SAM > v4s1_novo.sam the rest of the [[bash script
Alignment Results
# Read Sequences: 11450664 # Aligned: 4194879 # Unique Alignment: 4178621 # Gapped Alignment: 3042944 # Quality Filter: 23301 # Homopolymer Filter: 40 # Elapsed Time: 9373.277 (sec.) # CPU Time: 154.0 (min.) # Done at Tue Oct 15 16:24:52 2013
Error Counting Results
Error Rate: 6.63% Error Rate of Insertions: .179% Error Rate of Deletions: 2.36% Error Rate of Substitutions: 4.09%