AlleleSeq

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(General outline of pipeline)
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actual process.
actual process.
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1) '''Pre-processing - diploid genome construction using ''vcf2diploid'''''
+
1) '''Pre-processing - diploid genome construction using ''vcf2diploid''''' <br>
In the Rozowsky ''et al.'' (2011) paper, the
In the Rozowsky ''et al.'' (2011) paper, the
pre-processing step separate (phase) the child's diploid genome into its parental  
pre-processing step separate (phase) the child's diploid genome into its parental  
haplotypes based on the sequences of the parents.  
haplotypes based on the sequences of the parents.  
-
2) '''AlleleSeq pipeline - mapping and statistical testing using PIPELINE.mk package'''
+
2) '''AlleleSeq pipeline - mapping and statistical testing using PIPELINE.mk package''' <br>
  (a) Reads from ChIP-seq and RNA-seq experiments are aligned and mapped to both  
  (a) Reads from ChIP-seq and RNA-seq experiments are aligned and mapped to both  
haplotype genomes.
haplotype genomes.
Line 20: Line 20:
  (b) Then for each SNV position with mapped reads, we compare the allele  
  (b) Then for each SNV position with mapped reads, we compare the allele  
frequencies observed in the two parental haplotypes.
frequencies observed in the two parental haplotypes.
-
 
=vcf2diploid=
=vcf2diploid=

Revision as of 15:52, 7 June 2013

Contents


General outline of pipeline

The basic goal of the pipeline is to take a large collection of reads generated from ChIP-seq or RNA-seq experiments associated with an individual and detect single nucleotide variants (SNVs) that correspond to significantly skewed number of reads. To do this, the pipeline starts with a preprocessing step, before the actual process.

1) Pre-processing - diploid genome construction using vcf2diploid
In the Rozowsky et al. (2011) paper, the pre-processing step separate (phase) the child's diploid genome into its parental haplotypes based on the sequences of the parents.

2) AlleleSeq pipeline - mapping and statistical testing using PIPELINE.mk package

(a) Reads from ChIP-seq and RNA-seq experiments are aligned and mapped to both 

haplotype genomes.

(b) Then for each SNV position with mapped reads, we compare the allele 

frequencies observed in the two parental haplotypes.

vcf2diploid

AlleleSeq pipeline

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