Matt:LabNotes/2013-9-27
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V4S1 MimicError Novoalign to Full Reference[edit]
- Novoindex
novoindex V4S1_full.ndx V4S1_full.fa # novoindex (2.8) - Universal k-mer index constructor. # (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd # novoindex V4S1_full.ndx V4S1_full.fa # Creating 16 indexing threads. # Building with 7-mer and step of 1 bp. # novoindex construction dT = 0.2s # Index memory size 0.001Gbyte. # Done.
- Novoalign
novoalign -d V4S1_full.ndx -f V4S1_mockseq_error_mimic.fq -F STDFQ -r ALL -o SAM -o FULLNW > V4S1_50onFull_novoalign.sam & # Read Sequences: 2959000 # Aligned: 2953321 # Unique Alignment: 2949287 # Gapped Alignment: 395910 # Quality Filter: 4870 # Homopolymer Filter: 0 # Elapsed Time: 461.655 (sec.) # CPU Time: 7.4 (min.) # Done at Fri Sep 27 11:42:31 2013
- Samtools
samtools view -bS V4S1_50onFull_novoalign.sam | samtools sort - V4S1_50onFull_novoalign_sorted samtools view -h -F 4 -q 70 V4S1_50onFull_novoalign_sorted.bam > V4S1_50onFull_novoalign_sorted_filtered.sam samtools calmd -eS V4S1_50onFull_novoalign_sorted_filtered.sam /home/mzcai/DansProbes/V4S1_full.fa > V4S1_50onFull_novoalign_sf=.sam 192 Errors (eg [bam_fillmd1] different MD for read 'Mock': '20^C0^C30' -> '20^CC30')
- CountErrorNovoalign_perbase.pl does not work for this sam file because the read aligns somewhere from 28-33. I think since it is not revcomp that it's counting from the left end and since the probes aren't all uniform length, there's no way to do it this way
- I'll align to V4S1_fullrevcomp that way I know it should start after the read primer region (19bp)