Matt:LabNotes/2013-8-27: Difference between revisions

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>Mzcai
(Created page with "===Bowtie2 and Novoalign of Dan's MYcroArray Probes=== *Fastq Reads: /media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/fastq/ **V6S1:Lane 3 Index 11 **V4S1:Lane 2 Index 13 **V6S2:L...")
 
>Mzcai
No edit summary
Line 10: Line 10:
**V4S4:Lane 3 Index 12
**V4S4:Lane 3 Index 12
*Fasta Reference: /media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/probeseq/Probelist_all.fa
*Fasta Reference: /media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/probeseq/Probelist_all.fa
**V6S1:1-16559
{| {{table}}
**V4S1:16560-19518
| align="center" style="background:#f0f0f0;"|''''''
**V6S2:19519-35918
| align="center" style="background:#f0f0f0;"|'''start'''
**V4S2:35919-39518
| align="center" style="background:#f0f0f0;"|'''end'''
**V6S3:39519-52518
| align="center" style="background:#f0f0f0;"|'''x2'''
**V4S3:52519-58368
|-
**V6S4:58369-71682
| V6S1||1||16559||33118
**V4S4:71683-77669
|-
| V4S1||16560||19518||39036
|-
| V6S2||19519||35918||71836
|-
| V4S2||35919||39518||79036
|-
| V6S3||39519||52518||105036
|-
| V4S3||52519||58368||116736
|-
| V6S4||58369||71682||143364
|-
| V4S4||71683||77669||155338
|}
 
====Plan====
*Shorten reference file to 50bp with Editfasta.pl
*Separate probe reference into 8 sets
  head -33118 Probelist_50bp.fa > Probelist_V6S1.fa
  head -39036 Probelist_50bp.fa | tail -5918 > Probelist_V4S1.fa
  head -71836 Probelist_50bp.fa | tail -32800 > Probelist_V6S2.fa
  head -79036 Probelist_50bp.fa | tail -7200 > Probelist_V4S2.fa
  head -105036 Probelist_50bp.fa | tail -26000 > Probelist_V6S3.fa
  head -116736 Probelist_50bp.fa | tail -11700 > Probelist_V4S3.fa
  head -143364 Probelist_50bp.fa | tail -26628 > Probelist_V6S4.fa
  head -155338 Probelist_50bp.fa | tail -11974 > Probelist_V4S4.fa
*Build novoalign indexes for each
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S1.ndx Probelist_V6S1.fa
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S1.ndx Probelist_V4S1.fa
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S2.ndx Probelist_V6S2.fa
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S2.ndx Probelist_V4S2.fa
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S3.ndx Probelist_V6S3.fa
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S3.ndx Probelist_V4S3.fa
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S4.ndx Probelist_V6S4.fa
  /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S4.ndx Probelist_V4S4.fa
*Do end-to-end alignment with novoalign
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S1.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S1_novoalign.sam 2> V6S1_stderr.txt
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S1.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S1_novoalign.sam 2> V4S1_stderr.txt
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S2.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S2_novoalign.sam 2> V6S2_stderr.txt
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S2.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S2_novoalign.sam 2> V4S2_stderr.txt
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S3.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S3_novoalign.sam 2> V6S3_stderr.txt
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S3.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S3_novoalign.sam 2> V4S3_stderr.txt
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S4.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S4_novoalign.sam 2> V6S4_stderr.txt
  /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S4.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S4_novoalign.sam 2> V4S4_stderr.txt

Revision as of 00:03, 29 August 2013

Bowtie2 and Novoalign of Dan's MYcroArray Probes

  • Fastq Reads: /media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/fastq/
    • V6S1:Lane 3 Index 11
    • V4S1:Lane 2 Index 13
    • V6S2:Lane 3 Index 10
    • V4S2:Lane 3 Index 12
    • V6S3:Lane 3 Index 11
    • V4S3:Lane 2 Index 13
    • V6S4:Lane 3 Index 10
    • V4S4:Lane 3 Index 12
  • Fasta Reference: /media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/probeseq/Probelist_all.fa
' start end x2
V6S1 1 16559 33118
V4S1 16560 19518 39036
V6S2 19519 35918 71836
V4S2 35919 39518 79036
V6S3 39519 52518 105036
V4S3 52519 58368 116736
V6S4 58369 71682 143364
V4S4 71683 77669 155338

Plan

  • Shorten reference file to 50bp with Editfasta.pl
  • Separate probe reference into 8 sets
 head -33118 Probelist_50bp.fa > Probelist_V6S1.fa
 head -39036 Probelist_50bp.fa | tail -5918 > Probelist_V4S1.fa
 head -71836 Probelist_50bp.fa | tail -32800 > Probelist_V6S2.fa
 head -79036 Probelist_50bp.fa | tail -7200 > Probelist_V4S2.fa
 head -105036 Probelist_50bp.fa | tail -26000 > Probelist_V6S3.fa
 head -116736 Probelist_50bp.fa | tail -11700 > Probelist_V4S3.fa
 head -143364 Probelist_50bp.fa | tail -26628 > Probelist_V6S4.fa
 head -155338 Probelist_50bp.fa | tail -11974 > Probelist_V4S4.fa
  • Build novoalign indexes for each
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S1.ndx Probelist_V6S1.fa
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S1.ndx Probelist_V4S1.fa
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S2.ndx Probelist_V6S2.fa
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S2.ndx Probelist_V4S2.fa
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S3.ndx Probelist_V6S3.fa
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S3.ndx Probelist_V4S3.fa
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V6S4.ndx Probelist_V6S4.fa
 /home/kunzhang/softwares/Novocraft/novocraft/novoindex V4S4.ndx Probelist_V4S4.fa
  • Do end-to-end alignment with novoalign
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S1.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S1_novoalign.sam 2> V6S1_stderr.txt
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S1.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S1_novoalign.sam 2> V4S1_stderr.txt
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S2.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S2_novoalign.sam 2> V6S2_stderr.txt
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S2.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S2_novoalign.sam 2> V4S2_stderr.txt
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S3.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S3_novoalign.sam 2> V6S3_stderr.txt
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S3.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S3_novoalign.sam 2> V4S3_stderr.txt
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V6S4.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V6S4_novoalign.sam 2> V6S4_stderr.txt
 /home/kunzhang/softwares/Novocraft/novocraft/novoalign -d V4S4.ndx -f s_2_1_unassigned.txt -F ILMFQ -r ALL -o SAM -o FULLNW > V4S4_novoalign.sam 2> V4S4_stderr.txt