Daniel:Notebook/GenomeMiner/2013-8-13: Difference between revisions

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=HL155=
=HL155=
[[Daniel:Notebook/GenomeMiner|Back to Calendar]]


Continuing Matt's pipeline.  Looking over the perl script.
Continuing Matt's pipeline.  Looking over the perl script.
I believe I fixed the perl script (uses my notation):  [[File:Count_mismatch.txt]]
===Results===
'''Error Rate''': 2.08727984165367
{| class="wikitable" <hiddentext>generated with [[:de:Wikipedia:Helferlein/VBA-Macro for EXCEL tableconversion]] V1.8</hiddentext>
|- style="font-size:12pt" align="center"
| align="center" width="65" height="30" | &nbsp;
|style="font-weight:bold" width="65" | Total reads
|style="font-weight:bold" width="65" | Filtered reads
|style="font-weight:bold" width="65" | Perfect match
|style="font-weight:bold" width="65" | 1 ins/del
|style="font-weight:bold" width="65" | 1 sub
|style="font-weight:bold" width="65" | 2 ins/del
|style="font-weight:bold" width="65" | 2 sub
|style="font-weight:bold" width="65" | 1 ins/del & 1 sub
|style="font-weight:bold" align="center" width="65" | 3+
|- style="font-size:12pt" align="center"
|style="font-weight:bold" height="15" | Number
| align="center" | 20727275
| align="center" | 15082383
| align="center" | 4411040
| align="center" | 3584377
| align="center" | 2417322
| align="center" | 1893421
| align="center" | 754110
| align="center" | 1647242
| align="center" | 374871
|- style="font-size:12pt" align="center"
|style="font-weight:bold" height="15" | Percent
| align="center" | 100
| align="center" | 72.77
| align="center" | 21.28
| align="center" | 17.29
| align="center" | 11.66
| align="center" | 9.13
| align="center" | 3.64
| align="center" | 7.95
| align="center" | 1.81
|}
Comparing this against [[Matt:LabNotes/2013-8-9#Count mismatches of Agi26k0gap|Matt's results]], it looks like the MYcroarray probes have more errors.  Around 75% of Matt's reads were perfect, but mine tend to have at least 1 error (only around 20% perfect).
Also analyzed the results (partly).  [[Daniel:Notebook/GenomeMiner#HL155|See here]] for analysis.

Latest revision as of 23:58, 13 August 2013

HL155[edit]

Back to Calendar

Continuing Matt's pipeline. Looking over the perl script.

I believe I fixed the perl script (uses my notation): File:Count mismatch.txt

Results[edit]

Error Rate: 2.08727984165367

  Total reads Filtered reads Perfect match 1 ins/del 1 sub 2 ins/del 2 sub 1 ins/del & 1 sub 3+
Number 20727275 15082383 4411040 3584377 2417322 1893421 754110 1647242 374871
Percent 100 72.77 21.28 17.29 11.66 9.13 3.64 7.95 1.81

Comparing this against Matt's results, it looks like the MYcroarray probes have more errors. Around 75% of Matt's reads were perfect, but mine tend to have at least 1 error (only around 20% perfect).

Also analyzed the results (partly). See here for analysis.