Matt:LabNotes/2013-10-15: Difference between revisions
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===Count Nuclei App=== | ===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 | |||
[[]] | |||
*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 | |||
[[]] |
Revision as of 01:28, 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 %
- 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)
- 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
- 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
[[]]
- 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
[[]]