[ensembl-dev] GRCh37 Protein sequence has asterisks

Luke Goodsell l.goodsell at achillestx.com
Mon Dec 4 17:55:28 GMT 2017


Hi Allessandro,

Is there a way to extract the BAM-edited sequences? I'd simply like to get FASTA files of the RefSeq cDNA and proteins as used by VEP.

Kind regards,
Luke




From: Alessandro Vullo
Sent: Monday, 4 December, 17:44
Subject: Re: [ensembl-dev] GRCh37 Protein sequence has asterisks
To: Ensembl developers list, Luke Goodsell


Hi Luke, The problem is likely to depend on RefSeq differing from the reference. Are you using VEP and then retrieving the sequence as annotated by it? Quoting the relevant people (VEP): "VEP uses BAMs to correct RefSeqs that differ from the reference, and without those the API can give incorrect translations. This will hopefully be fixed in future when the SeqEdit objects that VEP creates from the BAMs are incorporated directly into the otherfeatures DB." Hope that helps, Alessandro

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