Daniel:Notebook/Haplotyping/SISSORPipeline: Difference between revisions

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[[Daniel:Notebook/Haplotyping|Back to Haplotyping Notebook]]
[[Daniel:Notebook/Haplotyping|Back to Haplotyping Notebook]]


The purpose of this section is to include data from my recreation/use of Eric's algorithm to properly segment SISSOR data.  Since SISSOR has very low coverage, the samtools targetcut function does not properly identify fragments created in the microfluidic device.
The purpose of this section is to include data from my recreation/use of Eric's algorithm to properly segment SISSOR data.  Since SISSOR has very low coverage, the samtools targetcut function does not properly identify fragments created in the microfluidic device.  Another important part of this is to make sure the output is consistent with the samtools targetcut format for easier combination with the BAC/Hi-C data for HAPCUT.


[[EricChu:LabNotesMDA/2014-4-16|Eric's Original Algorithm]]
[[EricChu:LabNotesMDA/2014-4-16|Eric's Original Algorithm]]
==Algorithm Overview==
#Python script for establishing bin read counts
#Cutoff to define initial states--may be a weak point
#Hidden Markov Model to smooth initial states to final states
#Produce a .sam format matching samtools targetcut--Extra step I need


==Calendar==
==Calendar==


<calendar>
<calendar>
name=Daniel:Notebook/Haplotyping
name=Daniel:Notebook/Haplotyping/SISSORPipeline
format=%name/%year-%month-%day
date=2015/02/01
view=oneyear
</calendar>
 
<calendar>
name=Daniel:Notebook/Haplotyping/SISSORPipeline
format=%name/%year-%month-%day
format=%name/%year-%month-%day
date=2014/02/01
date=2014/02/01
view=oneyear
view=oneyear
</calendar>
</calendar>

Latest revision as of 19:32, 3 February 2015

SISSOR Segmentation Pipeline[edit]

Back to Haplotyping Notebook

The purpose of this section is to include data from my recreation/use of Eric's algorithm to properly segment SISSOR data. Since SISSOR has very low coverage, the samtools targetcut function does not properly identify fragments created in the microfluidic device. Another important part of this is to make sure the output is consistent with the samtools targetcut format for easier combination with the BAC/Hi-C data for HAPCUT.

Eric's Original Algorithm

Algorithm Overview[edit]

  1. Python script for establishing bin read counts
  2. Cutoff to define initial states--may be a weak point
  3. Hidden Markov Model to smooth initial states to final states
  4. Produce a .sam format matching samtools targetcut--Extra step I need

Calendar[edit]

<calendar> name=Daniel:Notebook/Haplotyping/SISSORPipeline format=%name/%year-%month-%day date=2015/02/01 view=oneyear </calendar>

<calendar> name=Daniel:Notebook/Haplotyping/SISSORPipeline format=%name/%year-%month-%day date=2014/02/01 view=oneyear </calendar>