Daniel:Notebook/GenomeMiner/2013-10-8: Difference between revisions
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>Djacobse (Created page with "=HL155 Novoalign (Started 10/3/2013)= Back to Calendar ==V4S1== '''Calmd''' samtools calmd -eS no...") |
>Djacobse |
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'''Calmd''' | '''Calmd''' | ||
samtools calmd -eS novo_v4s1_sortfilt.sam V4S1_fullrevcomp.fa > novo_v4s1_sortfilteq.sam | 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== | |||
===Pipeline=== | |||
'''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=== | |||
# 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=== | |||
Error Rate: 5.47% | |||
Error Rate of Insertions: 2.40% | |||
Error Rate of Deletions: 1.96% | |||
Error Rate of Substitutions: 1.11% |
Latest revision as of 00:17, 9 October 2013
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%