Matt:LabNotes/2013-8-23

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Novoalign to repeat alignment of End Sequencing reads[edit]

  • Build index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex [options] [indexfile] [sequencefiles]
  • Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign [options]
    • /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d [indexfile] -f [readsfile] -F [readsfileformat] -r [reads_to_report] -o [outputfileformat] > [outputfile]
      • Readsfileformat: FA - fasta; ILMFQ - Illumina1.3+ Phred+64; STDFQ - Sanger Phred+33; SLXFQ - Solexa+64

CA12k[edit]

Build index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex /home/mzcai/CA12k_EndSequencing_Analysis/Novoalign/CAprobes_50bp.ndx /home/mzcai/CA12k_EndSequencing_Analysis/CAprobes_to_order_50bp.fa
Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/mzcai/CA12k_EndSequencing_Analysis/Novoalign/CAprobes_50bp.ndx -f /home/mzcai/CA12k_EndSequencing_Analysis/s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM > Readsalign2probes_CA_novoalign.sam

 #   Read Sequences: 29716630
 #            Aligned:  6607495
 #   Unique Alignment:  6586488
 #   Gapped Alignment:  2219484
 #     Quality Filter:   146500
 # Homopolymer Filter:      758
 #       Elapsed Time: 13736.789 (sec.)
 #           CPU Time: 225.9 (min.)
 # Done at Fri Aug 23 15:56:01 2013
  • This does a local alignment so CIGAR string contains 'S', which stands for soft-clipping
    • I want to avoid that since it will remove some of the synthesis errors we are trying to measure
    • Use -o FULLNW to do end-to-end alignment

Agi26k0gap[edit]

Build Index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k0gapprobes.ndx /home/mzcai/Agi26k_EndSequencing_Analysis/Agi26k0gap_corrected.fa

Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k0gapprobes.ndx -f /home/mzcai/Agi26k_EndSequencing_Analysis/s_3_1_Indx10.txt -F ILMFQ -r ALL -o SAM > /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Readsalign2probes_Agi26k0gap_novoalign.sam 2> /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/0gapstderr.txt &

 #     Read Sequences: 16368416
 #            Aligned:  6005917
 #   Unique Alignment:  6004799
 #   Gapped Alignment:  1727168
 #     Quality Filter:    56701
 # Homopolymer Filter:        9
 #       Elapsed Time: 13633.364 (sec.)
 #           CPU Time: 171.2 (min.)
 # Done at Fri Aug 23 20:32:11 201

Agi26k20gap[edit]

Build Index: /home/kunzhang/softwares/Novocraft/novocraft/novoindex /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k20gapprobes.ndx /home/mzcai/Agi26k_EndSequencing_Analysis/Agi26k20gap_corrected.fa

Align: /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Agi26k20gapprobes.ndx -f /home/mzcai/Agi26k_EndSequencing_Analysis/s_3_1_Indx12.txt -F ILMFQ -r ALL -o SAM > /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/Readsalign2probes_Agi26k20gap_novoalign.sam 2> /home/mzcai/Agi26k_EndSequencing_Analysis/Novoalign/20gapstderr.txt &

 #     Read Sequences: 17308686
 #            Aligned:  4798906
 #   Unique Alignment:  4794645
 #   Gapped Alignment:  1353496
 #     Quality Filter:    48231
 # Homopolymer Filter:       10
 #       Elapsed Time: 14327.598 (sec.)
 #           CPU Time: 180.0 (min.)
 # Done at Fri Aug 23 20:47:56 2013