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 |
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(2 intermediate revisions by the same user not shown) | |||
Line 22: | Line 22: | ||
***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 | ||
Line 29: | Line 29: | ||
***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)==== | ||
Line 52: | Line 52: | ||
***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 | ||
Line 59: | Line 59: | ||
***Ins: 0.229 % | ***Ins: 0.229 % | ||
***Sub: 0.107 % | ***Sub: 0.107 % | ||
[[]] | [[File:V4S1mock_losubhidel_Novoalign_FullRef_Filter_ErrorPerBase.JPG]] | ||
===Count Nuclei App=== | |||
*The reason the 16-bit images (converted from 8-bit) didn't work yesterday was because they were the cropped images (not raw) | |||
*Count Primary Rolonies from [[Hosuk:LabNotes/2013-10-9]] | |||
**File: Series021_20xobj-Zstack-2kx2k_MaxProject_Cy5-16bit | |||
**Min width: 0.7um; Max width: 2um; Intensity above local bg: 50 | |||
**42,019 Rolonies | |||
[[File:Series021_20xobj_2kx2k_Cy5_Count_Overlay.jpg]] | |||
*Count ACTB Target regions on Primary Rolonies | |||
**File: Series021_20xobj-Zstack-2kx2k_MaxProject_ATTO488-16bit | |||
**Min width: 0.7um; Max width: 2um; Intensity above local bg: 40 | |||
**312 Rolonies | |||
[[File:Series021_20xobj_2kx2k_ATTO488_Count_Overlay.jpg]] |
Latest revision as of 23:40, 16 October 2013
V4S1 Mock Reads with Novoalign Full Reference[edit]
Error 1% substitution only[edit]
- 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 %
- Bases 10-30 Average
File:V4S1mock sub1 Novoalign FullRef ErrorPerBase.JPG
- CountErrorNovoalignFullRefFilter_EachBase.pl
- Bases 10-30 Average
- Del: 0 %
- Ins: 6.48*10^-6 %
- Sub: 0.986033 %
- Bases 10-30 Average
File:V4S1mock sub1 Novoalign FullRef Filter ErrorPerBase.JPG
Low substitution High deletion (1.01% Del, 0.26% Sub, 0.05% Ins)[edit]
- 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 %
- Bases 10-30 Average
File:V4S1mock losubhidel Novoalign FullRef ErrorPerBase.JPG
- CountErrorNovoalignFullRefFilter_EachBase.pl
- Bases 10-30 Average
- Del: 0.932 %
- Ins: 0.229 %
- Sub: 0.107 %
- Bases 10-30 Average
File:V4S1mock losubhidel Novoalign FullRef Filter ErrorPerBase.JPG
Count Nuclei App[edit]
- The reason the 16-bit images (converted from 8-bit) didn't work yesterday was because they were the cropped images (not raw)
- Count Primary Rolonies from Hosuk:LabNotes/2013-10-9
- File: Series021_20xobj-Zstack-2kx2k_MaxProject_Cy5-16bit
- Min width: 0.7um; Max width: 2um; Intensity above local bg: 50
- 42,019 Rolonies
File:Series021 20xobj 2kx2k Cy5 Count Overlay.jpg
- Count ACTB Target regions on Primary Rolonies
- File: Series021_20xobj-Zstack-2kx2k_MaxProject_ATTO488-16bit
- Min width: 0.7um; Max width: 2um; Intensity above local bg: 40
- 312 Rolonies