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==Oligo Synthesis Error Rate: PhiX Control for determining Sequencing Error Rate== <!-- novoindex phix.ndx phixsequence.fa # novoindex (3.1) - Universal k-mer index constructor. # (C) 2008 - 2011 NovoCraft Technologies Sdn Bhd # novoindex phix.ndx phixsequence.fa # Creating 16 indexing threads. # Building with 6-mer and step of 1 bp. # novoindex construction dT = 0.1s # Index memory size 0.000Gbyte. # Done. novoalign -d phix.ndx -f s_1_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > PhiX_novoalign.sam & [1] 4260 mzcai@genome-miner:~/scratch/PhiX$ # License file: /home/dinh/softwares/novocraft/novoalign.lic # License expired on 3 Nov 2013. # System Local time: Fri Jun 6 12:47:26 2014 Warning: A reporting limit ( -r All limit )should be set with the -r All option. # novoalign (V3.01.02 - Build Sep 27 2013 @ 15:09:17 - A short read aligner with qualities. # (C) 2008,2009,2010,2011 NovoCraft Technologies Sdn Bhd. # License file: /home/dinh/softwares/novocraft/novoalign.lic # Licensed to Integrated Genomics@UC San Diego # novoalign -d phix.ndx -f s_1_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW # Starting at Fri Jun 6 12:47:26 2014 # Interpreting input files as Illumina FASTQ, Casava Pipeline 1.3 to 1.7. # Index Build Version: 3.1 # Hash length: 6 # Step size: 1 # Read Sequences: 1710082 # Aligned: 35 # Unique Alignment: 35 # Gapped Alignment: 0 # Quality Filter: 130945 # Homopolymer Filter: 464062 # Elapsed Time: 210.012 (secs.) # CPU Time: 3.42 (min.) # Done at Fri Jun 6 12:50:56 2014 samtools view -bS PhiX_novoalign.sam | samtools sort - PhiX_novoalign_sorted samtools view -h -F 4 -q 70 PhiX_novoalign_sorted.bam > PhiX_novoalign_sorted_filtered.sam !!!NO ALIGNMENTS!!!-->
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