Daniel:Notebook/GenomeMiner/2013-10-8
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HL155 Novoalign (Started 10/3/2013)[edit]
V4S1[edit]
Calmd
samtools calmd -eS novo_v4s1_sortfilt.sam V4S1_fullrevcomp.fa > novo_v4s1_sortfilteq.sam
Perl Script
perl count_mismatch.plx
Error Counting Results[edit]
Error Rate: 5.42% Error Rate of Insertions: 2.22% Error Rate of Deletions: 2.15% Error Rate of Substitutions: 1.05%
V4S2[edit]
Pipeline[edit]
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
Convert to Bam and Sort
samtools view -bS novo_v4s2.sam | samtools sort - novo_v4s2_sort
Filter
samtools view -h -F 4 -q 70 novo_v4s2_sort.bam > novo_v4s2_sortfilt.sam
Calmd
samtools calmd -eS novo_v4s2_sortfilt.sam V4S2_fullrevcomp.fa > novo_v4s2_sortfilteq.sam
Perl Error Counting Script
perl count_mismatch.plx
Alignment Results[edit]
# Read Sequences: 17308686 # Aligned: 3672898 # Unique Alignment: 3663803 # Gapped Alignment: 2517060 # Quality Filter: 44201 # Homopolymer Filter: 11 # Elapsed Time: 14209.542 (sec.) # CPU Time: 179.1 (min.) # Done at Tue Oct 8 14:17:27 2013
Error Counting Results[edit]
Error Rate: 5.47% Error Rate of Insertions: 2.40% Error Rate of Deletions: 1.96% Error Rate of Substitutions: 1.11%