AlleleSeq
From GersteinInfo
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(→General outline of pipeline) |
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actual process. | actual process. | ||
| - | 1) '''Pre-processing - diploid genome construction using ''vcf2diploid''''' <br> | + | (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. <br> |
| - | 2) '''AlleleSeq pipeline - mapping and statistical testing using PIPELINE.mk package''' <br> | + | (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. <br><br> |
(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. <br><br> |
=vcf2diploid= | =vcf2diploid= | ||
Revision as of 15:53, 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.
