Hi all, I am trying to figure out how to align loci to in silico digested fragments. I would like to map ~50,000 loci from an RRBS experiment back to the fragments which resulted from the restriction enzyme digestion, but I am not sure how to do it. My goal is to determine if the loci are localized to a particular fragment size and/or a particular location within each fragment (ends, middle).

I have found many software packages that do in silico restriction enzyme digestions on the whole genome, but so far I am only able to extract information about the length of the fragments and start/end locations, not create files (fasta files of each fragment?) which I can align my loci back onto. Are you aware of any way this can be done?

Thank you in advance!

Please take a look at the Bioconductor package REDseq (Restriction Enzyme Digestion followed by Sequencing) http://bioconductor.org/packages/release/bioc/html/REDseq.html. Hopefully this is what you are looking for. Best, Julie

From: "emb13 [bioc]" noreply@bioconductor.org Reply-To: "reply+8f4f2e30+code@bioconductor.org" <reply+8f4f2e30+code@bioconductor.org> Date: Friday, April 12, 2019 at 3:01 PM To: "Zhu, Lihua (Julie)" Julie.Zhu@umassmed.edu Subject: [bioc] How to align loci to in silico digested fragments

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Hi all, I am trying to figure out how to align loci to in silico digested fragments. I would like to map ~50,000 loci from an RRBS experiment back to the fragments which resulted from the restriction enzyme digestion, but I am not sure how to do it. My goal is to determine if the loci are localized to a particular fragment size and/or a particular location within each fragment (ends, middle).

I have found many software packages that do in silico restriction enzyme digestions on the whole genome, but so far I am only able to extract information about the length of the fragments and start/end locations, not create files (fasta files of each fragment?) which I can align my loci back onto. Are you aware of any way this can be done?

Thank you in advance!