<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi Luke,</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">There is no straightforward way to do this via Ensembl at the moment; I’d suggest you download the relevant files from NCBI.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">The BAM files we use are obtained from <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/GRCh37.p13_interim_annotation/">ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens/GRCh37.p13_interim_annotation/</a>; it seems there’s a protein and rna FASTA file in there which may have what you need.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Otherwise you may find what you need in the parent directory <a href="ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens">ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/H_sapiens</a>. I’m not familiar with NCBI’s FASTA layout so you’d have to investigate yourself!</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Regards</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Will McLaren</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Ensembl Variation</div> <br> <div id="bloop_sign_1512465073089561856" class="bloop_sign"></div> <br><p class="airmail_on">On 4 December 2017 at 5:55:38 pm, Luke Goodsell (<a href="mailto:l.goodsell@achillestx.com">l.goodsell@achillestx.com</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>
<title></title>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
Hi Allessandro,<br>
<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
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.<br>
<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
Kind regards,<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
Luke<br>
<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
<br>
<br>
<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
From: Alessandro Vullo<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
Sent: Monday, 4 December, 17:44<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
Subject: Re: [ensembl-dev] GRCh37 Protein sequence has
asterisks<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
To: Ensembl developers list, Luke Goodsell<br>
<br>
<br></div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black;">
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<br>
<br></div>
This e-mail message contains confidential information intended only
for the use of the individual or entity to which it is addressed.
If you are not the intended recipient, please do not disseminate,
distribute or copy this communication, by e-mail or otherwise.
Instead, please notify us immediately by return e-mail and then
delete and discard all copies of the e-mail. We have taken all
reasonable precautions to check this e-mail and any attachments for
viruses, but we cannot accept any liability for any damage
sustained as a result of any virus, worm or other malicious
software. Achilles Therapeutics Limited (10167668) is registered in
England and Wales. The registered office is at 215 Euston Road,
London, NW1 2BE, UK.
_______________________________________________
<br>Dev mailing list Dev@ensembl.org
<br>Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
<br>Ensembl Blog: http://www.ensembl.info/
<br></div></div></span></blockquote></body></html>