Matt:LabNotes/2013-10-15: Difference between revisions

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>Mzcai
(Created page with "===V4S1 Mock Reads with Novoalign Full Reference=== ====Error 1% substitution only==== *Align novoalign -d ../mimicerror/V4S1_fullrevcomp.ndx -f v4s1_mockseq_1s.fq -F STDFQ...")
 
>Mzcai
mNo edit summary
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***Ins: 0.001545 %
***Ins: 0.001545 %
***Sub: 0.985943 %
***Sub: 0.985943 %
[[]]
[[File:V4S1mock_sub1_Novoalign_FullRef_ErrorPerBase.JPG]]


*CountErrorNovoalignFullRefFilter_EachBase.pl
*CountErrorNovoalignFullRefFilter_EachBase.pl
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***Ins: 6.48*10^-6 %
***Ins: 6.48*10^-6 %
***Sub: 0.986033 %
***Sub: 0.986033 %
[[]]
[[File:V4S1mock_sub1_Novoalign_FullRef_Filter_ErrorPerBase.JPG]]


====Low substitution High deletion (1.01% Del, 0.26% Sub, 0.05% Ins)====
====Low substitution High deletion (1.01% Del, 0.26% Sub, 0.05% Ins)====
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***Ins: 0.285 %
***Ins: 0.285 %
***Sub: 0.106 %
***Sub: 0.106 %
[[]]
[[File:V4S1mock_losubhidel_Novoalign_FullRef_ErrorPerBase.JPG]]


*CountErrorNovoalignFullRefFilter_EachBase.pl
*CountErrorNovoalignFullRefFilter_EachBase.pl
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***Ins: 0.229 %
***Ins: 0.229 %
***Sub: 0.107 %
***Sub: 0.107 %
[[]]
[[File:V4S1mock_losubhidel_Novoalign_FullRef_Filter_ErrorPerBase.JPG]]
 
===Count Nuclei App===
*So it's possible the reason it didn't work before was because it was cropped (and therefore not

Revision as of 01:01, 16 October 2013

V4S1 Mock Reads with Novoalign Full Reference

Error 1% substitution only

  • Align
 novoalign -d ../mimicerror/V4S1_fullrevcomp.ndx -f v4s1_mockseq_1s.fq -F STDFQ -r ALL -o SAM -o FULLNW > v4s1_mockseq_1s_novoalign_fullrevcomp.sam &
 #     Read Sequences:  2959000
 #            Aligned:  2953594
 #   Unique Alignment:  2949594
 #   Gapped Alignment:     2816
 #     Quality Filter:     5048
 # Homopolymer Filter:        0
 #       Elapsed Time: 67.870 (secs.)
 #           CPU Time: 11.91 (min.)
 # Done at Tue Oct 15 11:22:00 2013
  • Samtools
 samtools view -bS v4s1_mockseq_1s_novoalign_fullrevcomp.sam | samtools sort - v4s1_mockseq_1s_novoalign_fullrevcomp_sorted
 samtools view -h -F 4 -q 70 v4s1_mockseq_1s_novoalign_fullrevcomp_sorted.bam > v4s1_mockseq_1s_novoalign_fullrevcomp_sorted_filtered.sam
 samtools calmd -eS v4s1_mockseq_1s_novoalign_fullrevcomp_sorted_filtered.sam /home/mzcai/DansProbes/V4S1_fullrevcomp.fa > v4s1_mockseq_1s_novoalign_fullrevcomp_sf=.sam
  • CountErrorNovoalignFullRef_EachBase.pl
    • Bases 10-30 Average
      • Del: 8.91*10^-5 %
      • Ins: 0.001545 %
      • Sub: 0.985943 %

File:V4S1mock sub1 Novoalign FullRef ErrorPerBase.JPG

  • CountErrorNovoalignFullRefFilter_EachBase.pl
    • Bases 10-30 Average
      • Del: 0 %
      • Ins: 6.48*10^-6 %
      • Sub: 0.986033 %

File:V4S1mock sub1 Novoalign FullRef Filter ErrorPerBase.JPG

Low substitution High deletion (1.01% Del, 0.26% Sub, 0.05% Ins)

  • Align
 novoalign -d ../mimicerror/V4S1_fullrevcomp.ndx -f v4s1_mockseq_error_losubhidel.fq -F STDFQ -r ALL -o SAM -o FULLNW > v4s1_mockseq_losubhidel_novoalign_fullrevcomp.sam &
 #     Read Sequences:  2959000
 #            Aligned:  2933687
 #   Unique Alignment:  2929681
 #   Gapped Alignment:  1256873
 #     Quality Filter:     4897
 # Homopolymer Filter:        0
 #       Elapsed Time: 96.893 (secs.)
 #           CPU Time: 19.85 (min.)
 # Done at Tue Oct 15 13:17:16 2013
  • Samtools
 samtools view -bS v4s1_mockseq_losubhidel_novoalign_fullrevcomp.sam | samtools sort - v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted
 samtools view -h -F 4 -q 70 v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted.bam > v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted_filtered.sam
 samtools calmd -eS v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sorted_filtered.sam /home/mzcai/DansProbes/V4S1_fullrevcomp.fa > v4s1_mockseq_losubhidel_novoalign_fullrevcomp_sf=.sam
  • CountErrorNovoalignFullRef_EachBase.pl
    • Bases 10-30 Average
      • Del: 0.935%
      • Ins: 0.285 %
      • Sub: 0.106 %

File:V4S1mock losubhidel Novoalign FullRef ErrorPerBase.JPG

  • CountErrorNovoalignFullRefFilter_EachBase.pl
    • Bases 10-30 Average
      • Del: 0.932 %
      • Ins: 0.229 %
      • Sub: 0.107 %

File:V4S1mock losubhidel Novoalign FullRef Filter ErrorPerBase.JPG

Count Nuclei App

  • So it's possible the reason it didn't work before was because it was cropped (and therefore not