Daniel:Notebook/GenomeMiner/2013-9-3: Difference between revisions

From ZhangLabWiki
Jump to navigation Jump to search
>Djacobse
>Djacobse
 
(One intermediate revision by the same user not shown)
Line 123: Line 123:


[[Image:Probecompare_Bargraph_HL155_08302013.png|800px]]
[[Image:Probecompare_Bargraph_HL155_08302013.png|800px]]
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.

Latest revision as of 23:04, 5 September 2013

HL155[edit]

Back to Calendar

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[edit]

  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[edit]

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[edit]

It's also important to count the probes again with the updated reverse complementary info.

Workflow[edit]

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[edit]

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.