From asma.rabe at gmail.com Wed Nov 11 16:58:26 2015 From: asma.rabe at gmail.com (asma.rabe at gmail.com) Date: Thu, 12 Nov 2015 01:58:26 +0900 Subject: [Bioperl-l] Get strand from pos Message-ID: <3C919385-3954-4E66-A233-DDB98A888946@gmail.com> Hi all, I have variant list and I would like to get the sequence and strand for each position. I could get sequence using Bio::DB::Fasta But I am not sure how to get strand information using position only ?? Any help is appreciated From cjfields at illinois.edu Wed Nov 11 17:57:00 2015 From: cjfields at illinois.edu (Fields, Christopher J) Date: Wed, 11 Nov 2015 17:57:00 +0000 Subject: [Bioperl-l] Get strand from pos In-Reply-To: <3C919385-3954-4E66-A233-DDB98A888946@gmail.com> References: <3C919385-3954-4E66-A233-DDB98A888946@gmail.com> Message-ID: <2A5D28B3-5246-4FDF-8BE9-ADD89FC36535@illinois.edu> Variant calls are made using a haploid reference genome for comparison and context (?+? strand, from 5? to 3?), so strand is normally not reported as everything is based on the ?+? strand. Offhand I don?t recall any VCF reports where strand is reported, and I?m struggling to think of a reason where this would be necessary. Maybe epigenmoic modifications on one strand (is that even reported in VCF)? chris On 11/11/15, 10:58 AM, "Bioperl-l on behalf of asma.rabe at gmail.com" wrote: > >Hi all, > >I have variant list and I would like to get the sequence and strand for each position. I could get sequence using Bio::DB::Fasta >But I am not sure how to get strand information using position only ?? > >Any help is appreciated > > > >_______________________________________________ >Bioperl-l mailing list >Bioperl-l at mailman.open-bio.org >http://mailman.open-bio.org/mailman/listinfo/bioperl-l