Hi,
I'm working on creating simple pipeline for allelic imbalance analysis for our lab. We want to analyze allelic imbalance for F1 crosses between two mice strains (CAST-EiJ and 129S1-SvlmJ). So one allele comes from CAST-EiJ genome, the second one from 129S1-SvlmJ. I need to map reads to two alleles and then run different tests.
The first issue is reference mapping bias. To overcome this bias, I want to use variant-aware aligner GSNAP. It requires one fasta sequence (considered as 'reference' for this task) and a list of SNPs between two alleles (it my case, this is the same as SNPs between two strains). I have two fasta files with sequences for mice strains. I also downloaded VCF files for both strains, but these VCF files describe difference between our strains and reference genome, mm10. So I probably need to create my own VCF file just from two fasta sequences. Could you please help me here? Do I need to write my own script to do this (probably align and list differences) or there is a program to do this?
Or maybe I'm complicating things and all this can be done other way? Thank a lot!
I'm working on creating simple pipeline for allelic imbalance analysis for our lab. We want to analyze allelic imbalance for F1 crosses between two mice strains (CAST-EiJ and 129S1-SvlmJ). So one allele comes from CAST-EiJ genome, the second one from 129S1-SvlmJ. I need to map reads to two alleles and then run different tests.
The first issue is reference mapping bias. To overcome this bias, I want to use variant-aware aligner GSNAP. It requires one fasta sequence (considered as 'reference' for this task) and a list of SNPs between two alleles (it my case, this is the same as SNPs between two strains). I have two fasta files with sequences for mice strains. I also downloaded VCF files for both strains, but these VCF files describe difference between our strains and reference genome, mm10. So I probably need to create my own VCF file just from two fasta sequences. Could you please help me here? Do I need to write my own script to do this (probably align and list differences) or there is a program to do this?
Or maybe I'm complicating things and all this can be done other way? Thank a lot!
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