Daniel:Notebook/GenomeMiner/2013-9-3
HL155
Matt discovered that the MYcroarray probe set may not be aligning well due because we should be aligning to the reverse complement of the probe sequences we've been using. As such, Matt did the analysis, and the results changed fairly dramatically.
Error Comparison
V4S1 | V4S2 | V4S3 | V4S4 | V6S1 | V6S2 | V6S3 | V6S4 | Weighted Average (%) | |
Overall Error Rate | 1.33% | 1.32% | 1.32% | 1.19% | 1.17% | 1.13% | 1.18% | 1.15% | 1.19 |
Insertions | 0.26% | 0.21% | 0.24% | 0.24% | 0.19% | 0.18% | 0.19% | 0.21% | 0.20 |
Deletions | 0.05% | 0.04% | 0.04% | 0.05% | 0.04% | 0.04% | 0.04% | 0.05% | 0.04 |
Substitutions | 1.01% | 1.07% | 1.04% | 0.90% | 0.94% | 0.91% | 0.95% | 0.89% | 0.94 |
Number of Probes | 2959 | 3600 | 5850 | 5987 | 16559 | 16400 | 13000 | 13314 |
Updated Error Comparison
File:AgilentMYCA ErrorComp090313.png
So now MYcroarray is still the worst of the three companies, but does not have nearly as bad of error.
Probecounts
It's also important to count the probes again with the updated reverse complementary info.
Workflow
Repeated for every set
Print 3rd Column (Name Column)
awk '{print $3}' V4S1_bowtie2_filt.sam > /media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/unfilt_revcomp_Matt/v4s1_list.txt
Substitute Matt's probe names for mine (for perl script)
:%s/Probe/Probe_v4s1_/g
Perl Script File:Probecount by set.txt
perl probecount_by_set.plx > v4s1_revcomp.csv
Copy to my computer for MATLAB analysis
scp djacobse@132.239.135.41:/media/LTS_15T/DEJ_LTS/SeqStore/130628_HL155/revcomp_probecounts_Matt/v4s1_rc_unfilt.csv ./
HL155_Master.m; switches 9,10,11
Counting Results
Individual Histograms
File:Hl155 filterrevcomp mycro bar.png
Company Comparison
File:Hl155 compare rc filt090313.png
Again, the results look at least marginally better. Compare this with the same analysis on the non-reverse complementary data:
File:Probecompare Bargraph HL155 08302013.png
The comparison shows that the normal counts are still the majority. There are also far fewer zeros. Combining this with the error comparison data, it looks as though MYcroarray is not such a terrible option now.