How to do allele specific expression analysis (ASE)
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23 days ago

Hello, I have RNA-seq data from an F1 hybrid, as well as the genomic sequences from both the paternal and maternal parents. I want to conduct Allele-Specific Expression (ASE) analysis of F1 hybrid to determine how the expression of alleles from each parent differs. Thank you for your help!

ASE • 396 views
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23 days ago
dsull ★ 7.2k

Obtain the VCF files containing the SNPs that distinguish your species from the reference genome, then run STAR with the WASP workflow (see the STAR manual for details).

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Thank you ! I will try it!

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Hello, I have other question, how can I obtain the VCF files containing the SNPs that distinguish two species? Thank you !

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You usually download it somewhere. I don’t know what species you are working with, so search around.

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how can I obtain the VCF files containing the SNPs that distinguish two species?

Based on the original question you are not working with two species but an F1 hybrid. Since you have genome sequence data from the two parents you could create these VCF's yourself as long as a good reference genome for your organism is available.

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