Question: How to align loci to in silico digested fragments
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gravatar for emb13
9 weeks ago by
emb130
emb130 wrote:

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!

in silico digestion • 91 views
ADD COMMENTlink modified 9 weeks ago by Julie Zhu4.0k • written 9 weeks ago by emb130
Answer: How to align loci to in silico digested fragments
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gravatar for Julie Zhu
9 weeks ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:

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

Activity on a post you are following on support.bioconductor.orghttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org&d=DwMCaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=r88SRGDLwte8pBgivGkDM9BL7VqLFKcUqUvATo4uHFk&s=IMRhMQKGg_ekS9ihfUctp_wgJKFevWSjHqJIL0M98l4&e=

User emb13https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_u_18397_&d=DwMCaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=r88SRGDLwte8pBgivGkDM9BL7VqLFKcUqUvATo4uHFk&s=HvM8xAITj-GB37vMLQS4VeczPAgVraOkk77lu1v_Ox8&e= wrote Question: How to align loci to in silico digested fragmentshttps://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_120075_&d=DwMCaQ&c=WJBj9sUF1mbpVIAf3biu3CPHX4MeRjY_w4DerPlOmhQ&r=3IbW-yoIQpGZOKgd4i2bgmPHhwHHF5gJMlij5cC5bLU&m=r88SRGDLwte8pBgivGkDM9BL7VqLFKcUqUvATo4uHFk&s=5scI9lLd1uBzpFXXGHCrH7zDPNt1wlhv7wDHFSH1k9o&e=:

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!

ADD COMMENTlink written 9 weeks ago by Julie Zhu4.0k
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