Daniel:Notebook/GenomeMiner/2013-10-8
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HL155 Novoalign (Started 10/3/2013)
V4S1
Calmd
samtools calmd -eS novo_v4s1_sortfilt.sam V4S1_fullrevcomp.fa > novo_v4s1_sortfilteq.sam
Perl Script
perl count_mismatch.plx
Error Counting Results
Error Rate: 5.42% Error Rate of Insertions: 2.22% Error Rate of Deletions: 2.15% Error Rate of Substitutions: 1.05%
V4S2
Build Index
novoindex index_v4s2fullrevcomp.ndx V4S2_fullrevcomp.fa
Novoalign
novoalign -d index_v4s2fullrevcomp.ndx -f ../../s_3_1_Indx12.txt -F ILMFQ -r ALL -o SAM -o FULLNW > novo_v4s2.sam