Matt:LabNotes/2013-8-23
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
- /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d [indexfile] -f [readsfile] -F [readsfileformat] -r [reads_to_report] -o [outputfileformat] > [outputfile]
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