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Investigating differentially expressed genes

Hello,

I'm analysing some rna-seq data and have determined a list of differentially expressed genes. I also have a list of SNP's from a recent GWAS study and have determined a 2Mb threshold for each variant (+/- 1Mb).

I would like to investigate whether any of my differentially expressed genes fall within these 2Mb thresholds. Does anybody have any ideas on how I can do this? I'm inclined to use BioMart but I'm unsure how for this purpose. There are about 900 SNP's in total.

Thanks in advance!

rna-seq gene r snp
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written by vanessaward876 • vanessaward876

Do you have the loci of each SNP in a file? Also reference genome builds may play a role here - are they different between the RNAseq and GWAS platform?

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written by andrew.j.skelton73 andrew.j.skelton73

You can most probably do that with bedtools

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written by WouterDeCoster WouterDeCoster

1 answer

Thanks! I used bedtools (galaxy version) and it seems to be working!

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written by vanessaward876 • vanessaward876

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