<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><base href="x-msg://98/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Ben,<div>The coordinates of your reads in the bam file should be genomic so there is no easy way. You will need to a write a Perl script to modify your bam file.</div><div>As you used Ensembl gene models the transformation of your coordinates should be pretty easy as the reference name in your bam file should be the stable id of your feature. Then you can get the genomic coordinates of the feature with the Perl API and calculate the genomic coordinates of your read.</div><div><br></div><div>Hope this help</div><div>Thibaut</div><div><br><div><div>On 22 Aug 2013, at 01:30, Ben Warren <<a href="mailto:Ben.Warren@plantandfood.co.nz">Ben.Warren@plantandfood.co.nz</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-NZ" link="blue" vlink="purple" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="WordSection1" style="page: WordSection1; "><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Hi,<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I have a RNA-<span class="SpellE">Seq</span><span class="Apple-converted-space"> </span>alignment, in the form of a BAM file, where the<span class="Apple-converted-space"> </span><span class="SpellE">reads</span><span class="Apple-converted-space"> </span>are aligned to gene models, which correspond to the stable ids of gene features in my local Ensembl instance.<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Is there any way to display the BAM in Ensembl? i.e. is it possible to display this BAM which references Ensembl gene features, not the scaffolds or<span class="Apple-converted-space"> </span><span class="SpellE">contigs</span><span class="Apple-converted-space"> </span>in a Ensembl assembly/coordinate-system?<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Cheers<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Ben<o:p></o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><b><span style="font-size: 10pt; font-family: Arial, sans-serif; ">Ben Warren</span></b><span style="font-size: 10pt; font-family: Arial, sans-serif; "><o:p></o:p></span></div></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 10pt; font-family: Arial, sans-serif; ">Research Technologist<o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; font-family: 'Times New Roman', serif; "> </span></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span><img width="210" height="70" id="_x0000_i1025" src="file:///C:\Users\hrabxw\AppData\Roaming\Microsoft\Signatures\PFR-LOGO.gif" alt="Plant & Food Research"></span><span><o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span> </span></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 8.5pt; font-family: Arial, sans-serif; ">F: +64 9 925 7001<br><a href="mailto:ben.warren@plantandfood.co.nz" style="color: purple; text-decoration: underline; ">ben.warren@plantandfood.co.nz</a><br><a href="http://www.plantandfood.co.nz" style="color: purple; text-decoration: underline; ">www.plantandfood.co.nz</a><br>The New Zealand Institute for Plant & Food Research Limited<o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><span style="font-size: 12pt; font-family: 'Times New Roman', serif; "> </span></div><div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; ">Postal Address:</span></b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; "><span class="Apple-converted-space"> </span>Plant & Food Research Mt Albert<br>Private Bag 92169, Auckland, 1142, New Zealand<br></span><b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; ">Physical Address:</span></b><span style="font-size: 8.5pt; font-family: Arial, sans-serif; "><span class="Apple-converted-space"> </span>Plant & Food Research Mt Albert<br>120 Mt Albert Road, Sandringham, Auckland, 1025, New Zealand<o:p></o:p></span></div></div><div style="margin: 0mm 0mm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div></div><table><tbody><tr><td bgcolor="#ffffff"><font><pre>The contents of this e-mail are confidential and may be subject to legal privilege.
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