<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Kamil,<div><br></div><div><div>Yes, the Ensembl patch pipeline does allow us to annotate genes where part a gene lies outside of the patch.</div></div><div><br></div><div>The features that you see lying outside of the patch coordinates are the two long transcripts <a href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000269512;r=HG375_PATCH:103810996-105012100;t=ENST00000594988" style="color: rgb(0, 0, 102); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 13px; text-align: center; white-space: nowrap; background-color: rgb(255, 255, 255); ">ENST00000594988</a> and <a href="http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000269512;r=HG375_PATCH:103810996-105012100;t=ENST00000593441" style="color: rgb(204, 0, 0); font-family: 'Luxi Sans', Helvetica, Arial, Geneva, sans-serif; font-size: 13px; text-align: center; white-space: nowrap; background-color: rgb(255, 255, 255); ">ENST00000593441</a> from gene IL1RAPL2. You can see them spanning across both sides of the patch here:</div><div><a href="http://www.ensembl.org/Homo_sapiens/Share/a902f2d99653b079b5c39f494fec090c102145539">http://www.ensembl.org/Homo_sapiens/Share/a902f2d99653b079b5c39f494fec090c102145539</a></div><div><br></div><div>In Ensembl, we are annotating and displaying the assembly patches within a genomic context; in the picture link above you will see that HG375_PATCH (green) is embedded within chromosome X. </div><div><br></div><div>This means that we have the DNA from chromosome X, both up- and downstream of HG375_PATCH, available at the time of annotating the patch. Annotating the patch within its genomic context means that we are able to annotate genes that span across the boundary of a patch. </div><div><br></div><div>Hope that helps,</div><div>Bronwen</div><div><br></div><div><br><div><div>On 14 Aug 2013, at 17:26, Kamil Slowikowski <<a href="mailto:kslowikowski@gmail.com">kslowikowski@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:14px">There exist features outside the coordinates listed for HG375_PATCH. I'm wondering if this is expected or if this is an error.</span><br><div style="font-family:arial,sans-serif;font-size:14px">

<br></div><div style="font-family:arial,sans-serif;font-size:14px"><br></div><div style="font-family:arial,sans-serif;font-size:14px"><a href="ftp://ftp.ensembl.org/pub/release-72/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.72.dna.chromosome.HG375_PATCH.fa.gz" target="_blank">ftp://ftp.<span class="" style="background-color:rgb(255,255,204);color:rgb(34,34,34)">ensembl</span>.org/pub/release-72/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.72.dna.chromosome.HG375_PATCH.fa.gz</a></div>

<div style="font-family:arial,sans-serif;font-size:14px"><br></div><div style="font-family:arial,sans-serif;font-size:14px"><font face="courier new, monospace">zcat Homo_sapiens.GRCh37.72.dna.chromosome.HG375_PATCH.fa.gz | head -n1</font></div>

<div style="font-family:arial,sans-serif;font-size:14px"><font face="courier new, monospace">>HG375_PATCH dna:chromosome chromosome:GRCh37:HG375_PATCH:104423968:104489001:1 PATCH_FIX</font></div><div style="font-family:arial,sans-serif;font-size:14px">

<br></div><div style="font-family:arial,sans-serif;font-size:14px">Notice that the last position is 104489001.</div><div style="font-family:arial,sans-serif;font-size:14px"><br></div><div style="font-family:arial,sans-serif;font-size:14px">

<br></div><div style="font-family:arial,sans-serif;font-size:14px"><a href="ftp://ftp.ensembl.org/pub/release-72/gtf/homo_sapiens/Homo_sapiens.GRCh37.72.gtf.gz" target="_blank">ftp://ftp.<span class="" style="background-color:rgb(255,255,204);color:rgb(34,34,34)">ensembl</span>.org/pub/release-72/gtf/homo_sapiens/Homo_sapiens.GRCh37.72.gtf.gz</a></div>

<div style="font-family:arial,sans-serif;font-size:14px"><br></div><div style="font-family:arial,sans-serif;font-size:14px"><div><font face="courier new, monospace">zcat Homo_sapiens.GRCh37.72.gtf.gz | grep HG375_PATCH | cut -f1-5 | head</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>exon<span style="white-space:pre-wrap">    </span>103810996<span style="white-space:pre-wrap">       </span>103811732</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>exon<span style="white-space:pre-wrap">    </span>103903576<span style="white-space:pre-wrap">       </span>103903676</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>CDS<span style="white-space:pre-wrap">     </span>103903595<span style="white-space:pre-wrap">       </span>103903676</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>start_codon<span style="white-space:pre-wrap">     </span>103903595<span style="white-space:pre-wrap">       </span>103903597</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>exon<span style="white-space:pre-wrap">    </span>104440157<span style="white-space:pre-wrap">       </span>104440430</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>CDS<span style="white-space:pre-wrap">     </span>104440157<span style="white-space:pre-wrap">       </span>104440430</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>exon<span style="white-space:pre-wrap">    </span>104478500<span style="white-space:pre-wrap">       </span>104478686</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>CDS<span style="white-space:pre-wrap">     </span>104478500<span style="white-space:pre-wrap">       </span>104478686</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>exon<span style="white-space:pre-wrap">    </span>104512069<span style="white-space:pre-wrap">       </span>104512222</font></div>

<div><font face="courier new, monospace">HG375_PATCH<span style="white-space:pre-wrap">   </span>protein_coding<span style="white-space:pre-wrap">  </span>CDS<span style="white-space:pre-wrap">     </span>104512069<span style="white-space:pre-wrap">       </span>104512222</font></div>

</div><div style="font-family:arial,sans-serif;font-size:14px"><font face="courier new, monospace"><br></font></div><span style="font-family:arial,sans-serif;font-size:14px">Notice the positions such as 104512069 are greater than 104489001.</span><br>

</div>
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