<div dir="ltr">sm = soft masked (i.e. repeats in lower case).<div><br></div><div>He may be looking at the 'genome' file, which is a mix of all 'toplevel' sequence. i.e. you can point him here:</div><div><a href="ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/hordeum_vulgare/dna/README">ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/hordeum_vulgare/dna/README</a><br></div><div><br></div><div><br></div><div>Cheers,</div><div>Dan.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 10 March 2015 at 20:13, Marcela K. Monaco <span dir="ltr"><<a href="mailto:mmonaco@cshl.edu" target="_blank">mmonaco@cshl.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi Dan,<br><br></div>About the assembly data for barley, I understand that this is more like a gene-ome and not a true assembly... But why is the user refering to contigs? I see a single pseudomolecule per file (with lost of Ns nonetheless)... <br><br>Also rm = repeat masked, and sm = ? <br></div><br></div>Thanks,<br><br></div>Marcela<br><div><div><div><br><div><div><div><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername"><a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a></b> <span dir="ltr"><<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>></span><br>Date: Tue, Mar 10, 2015 at 3:36 PM<br>Subject: [Feedback] Site Feedback: linke to balrey genome sequence<br>To: "<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>" <<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>><br>Cc: "Steve Larson [USDA ARS]" <<a href="mailto:Steve.Larson@ars.usda.gov" target="_blank">Steve.Larson@ars.usda.gov</a>><br><br><br>URL : <a href="http://ensembl.gramene.org/Hordeum_vulgare/Info/Index" target="_blank">http://ensembl.gramene.org/Hordeum_vulgare/Info/Index</a><br>
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Subject : Site Feedback: linke to balrey genome sequence<br>
<br>
Name : Steve Larson<br>
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Email : <a href="mailto:Steve.Larson@ars.usda.gov" target="_blank">Steve.Larson@ars.usda.gov</a><br>
<br>
Organization: USDA ARS<br>
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Comments :<br>
<br>
I think the link to the barley genome sequence assembly (File:Hordeum_vulgare.082214v1.25.dna.genome.fa.gz)<br>
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at<br>
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Index of <a href="ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/hordeum_vulgare/dna/" target="_blank">ftp://ftp.ensemblgenomes.org/pub/plants/release-25/fasta/hordeum_vulgare/dna/</a><br>
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is incorrect. This believe this file should contain about 20 psuedomolecules, not 10,000 contigs<br>
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<a href="http://www.warelab.org/bugs/view.php?id=5129" target="_blank">http://www.warelab.org/bugs/view.php?id=5129</a><br>
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