Matt:LabNotes/2013-10-15
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V4S1 Mock Reads with Novoalign Full Reference
Error 1% substitution only
- Align
novoalign -d ../mimicerror/V4S1_fullrevcomp.ndx -f v4s1_mockseq_1s.fq -F STDFQ -r ALL -o SAM -o FULLNW > v4s1_mockseq_1s_novoalign_fullrevcomp.sam & # Read Sequences: 2959000 # Aligned: 2953594 # Unique Alignment: 2949594 # Gapped Alignment: 2816 # Quality Filter: 5048 # Homopolymer Filter: 0 # Elapsed Time: 67.870 (secs.) # CPU Time: 11.91 (min.) # Done at Tue Oct 15 11:22:00 2013
- Samtools
samtools view -bS v4s1_mockseq_1s_novoalign_fullrevcomp.sam | samtools sort - v4s1_mockseq_1s_novoalign_fullrevcomp_sorted samtools view -h -F 4 -q 70 v4s1_mockseq_1s_novoalign_fullrevcomp_sorted.bam > v4s1_mockseq_1s_novoalign_fullrevcomp_sorted_filtered.sam samtools calmd -eS v4s1_mockseq_1s_novoalign_fullrevcomp_sorted_filtered.sam /home/mzcai/DansProbes/V4S1_fullrevcomp.fa > v4s1_mockseq_1s_novoalign_fullrevcomp_sf=.sam
- CountErrorNovoalignFullRef_EachBase.pl
- Bases 10-30 Average
- Del: 8.91*10^-5 %
- Ins: 0.001545 %
- Sub: 0.985943 %
- Bases 10-30 Average
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- CountErrorNovoalignFullRefFilter_EachBase.pl
- Bases 10-30 Average
- Del: 0 %
- Ins: 6.48*10^-6 %
- Sub: 0.986033 %
- Bases 10-30 Average
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Low substitution High deletion (1.01% Del, 0.26% Sub, 0.05% Ins)
- Align
novoalign -d ../mimicerror/V4S1_fullrevcomp.ndx -f v4s1_mockseq_error_losubhidel.fq -F STDFQ -r ALL -o SAM -o FULLNW > v4s1_mockseq_losubhidel_novoalign_fullrevcomp.sam & # Read Sequences: 2959000 # Aligned: 2933687 # Unique Alignment: 2929681 # Gapped Alignment: 1256873 # Quality Filter: 4897 # Homopolymer Filter: 0 # Elapsed Time: 96.893 (secs.) # CPU Time: 19.85 (min.) # Done at Tue Oct 15 13:17:16 2013
- Samtools
samtools view -bS v4s1_mockseq_losubhidel_novoalign_fullrevcomp.sam | samtools sort - v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted samtools view -h -F 4 -q 70 v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted.bam > v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted_filtered.sam samtools calmd -eS v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted_filtered.sam /home/mzcai/DansProbes/V4S1_fullrevcomp.fa > v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sf=.sam
- CountErrorNovoalignFullRef_EachBase.pl
- Bases 10-30 Average
- Del: 0.935%
- Ins: 0.285 %
- Sub: 0.106 %
- Bases 10-30 Average
[[]]
- CountErrorNovoalignFullRefFilter_EachBase.pl
- Bases 10-30 Average
- Del: 0.932 %
- Ins: 0.229 %
- Sub: 0.107 %
- Bases 10-30 Average
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