<div dir="ltr"><span id="m_3000834463988989175gmail-docs-internal-guid-a89e73dd-7bc6-f038-25b6-2085350846d0"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">BioSB RNA-seq data analysis course (7</span><span style="font-size:6pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:super;white-space:pre-wrap">th</span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap"> edition)</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Date:</span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap"> 6-8 November 2017</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Location:</span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap"> Leiden University Medical Center, the Netherlands</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Course coordinators: </span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Peter-Bram ‘t Hoen (LUMC), Leon Mei (LUMC), Jan Oosting (LUMC), Szymon Kielbasa (LUMC) </span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Course website:</span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap"> </span><a href="http://biosb.nl/education/course-portfolio/rna-seq/" style="text-decoration-line:none" target="_blank"><span style="font-size:10pt;font-family:Arial;background-color:transparent;text-decoration-line:underline;vertical-align:baseline;white-space:pre-wrap">http://biosb.nl/education/<wbr>course-portfolio/rna-seq/</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap"> . </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Registration: </span><a href="http://biosb.nl/education/course-portfolio/rna-seq/enrollment-rna-seq-2017/" style="text-decoration-line:none" target="_blank"><span style="font-size:10pt;font-family:Arial;background-color:transparent;text-decoration-line:underline;vertical-align:baseline;white-space:pre-wrap">http://biosb.nl/education/<wbr>course-portfolio/rna-seq/<wbr>enrollment-rna-seq-2017/</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap"> </span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Course description</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">The BioSB research school and partner LUMC are organizing a 3-day course on RNA-seq data analysis. This is an advanced course for people with experience in NGS. The course will consist of lectures, Galaxy and R practicals and will cover the analysis pipelines for differential transcript expression and variant calling. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects.</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap"> </span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Course topics </span></p><br><ul style="margin-top:0pt;margin-bottom:0pt"><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">RNA-seq experimental approaches and study design</span></p></li><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Quality control and alignment</span></p></li><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Statistics for differential gene expression</span></p></li><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">eQTL analysis and allele specific expression</span></p></li><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Single cell RNA sequencing</span></p></li><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Fusion transcript detection</span></p></li><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Small RNA profiling</span></p></li><li dir="ltr" style="list-style-type:disc;font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline"><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Software for RNA-seq data analysis</span></p></li></ul><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">Target audience</span></p><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. </span><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:700;vertical-align:baseline;white-space:pre-wrap">NB: The practicals are mostly in R. We require that participants have at least basic knowledge of R and experience in running R scripts. Participants must bring own laptops capable of running RStudio. Please download and install RStudio before the course. For Galaxy tutorial, please install firefox or google chrome web browser.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed.Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded projects </span><a href="http://rd-connect.eu/" style="text-decoration-line:none" target="_blank"><span style="font-size:10pt;font-family:Arial;background-color:transparent;text-decoration-line:underline;vertical-align:baseline;white-space:pre-wrap">RD-Connect</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap"> and </span><a href="https://www.bbmri.nl/" style="text-decoration-line:none" target="_blank"><span style="font-size:10pt;font-family:Arial;background-color:transparent;text-decoration-line:underline;vertical-align:baseline;white-space:pre-wrap">BBMRI-NL</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">This course is part of the</span><a href="http://biosb.nl/education/course-portfolio-2/" style="text-decoration-line:none" target="_blank"><span style="font-size:10pt;font-family:Arial;background-color:transparent;text-decoration-line:underline;vertical-align:baseline;white-space:pre-wrap"> Education Programme of BioSB</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">, the Netherlands Bioinformatics and Systems Biology Research School, which offers training and education for in bioinformatics and systems biology.</span></p><br><p dir="ltr" style="line-height:1.38;margin-top:0pt;margin-bottom:0pt"><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">More information about BioSB can be found at</span><a href="http://www.biosb.nl/" style="text-decoration-line:none" target="_blank"><span style="font-size:10pt;font-family:Arial;background-color:transparent;text-decoration-line:underline;vertical-align:baseline;white-space:pre-wrap"> www.biosb.nl</span></a><span style="font-size:10pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;vertical-align:baseline;white-space:pre-wrap">.</span></p><br></span><div><div class="m_3000834463988989175gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div dir="ltr"><div style="word-wrap:break-word"><font face="Arial Unicode MS" color="#484848" style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><div><span style="font-size:12px"><b><div style="font-family:"trebuchet ms",sans-serif;font-size:small;display:inline"></div></b></span><b style="font-size:12px"><div style="font-family:"trebuchet ms",sans-serif;font-size:small;display:inline"></div></b></div></font><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;word-wrap:break-word"><font face="Arial Unicode MS" color="#484848"><div><span style="font-size:12px"><b>Femke Francissen</b></span></div><div style="font-size:14px"><span style="font-size:12px">Community manager</span></div><div style="font-size:14px"><span style="font-size:12px">BioSB Research School</span><br></div><div style="font-size:14px"></div><div style="font-size:14px"><br></div><div style="font-size:14px"><div><font face="Arial Unicode MS"><span style="font-size:12px"><i><font color="#ff0000">NEW </font><font color="#000000">V</font></i></span></font><span style="font-style:italic;font-size:12px">isiting address (as of 1 July 2017): </span><span style="font-size:12px">Jaarbeurs Innovation Mile (JIM) </span><span style="font-size:12px">| 6th floor Beatrixgebouw</span><span style="font-size:12px"> </span><span style="font-size:12px">| </span><span style="font-size:12px">Jaarbeursplein 6 | </span><span style="font-size:12px">3521 AL Utrecht</span><br></div><div><div style="color:rgb(0,0,0);font-family:Calibri;font-size:medium;border-collapse:separate"><i style="color:rgb(34,34,34);font-family:"Arial Unicode MS";font-size:12px"><font color="#ff0000">NEW </font></i><font color="#484848" face="Arial Unicode MS"><span style="font-size:12px"><i>Postal address </i></span></font><span style="color:rgb(72,72,72);font-style:italic;font-family:"Arial Unicode MS";font-size:12px">(as of 1 July 2017): </span><span style="font-size:12px;color:rgb(72,72,72);font-family:"Arial Unicode MS"">Postbus 8500 | </span><span style="font-size:12px;color:rgb(72,72,72);font-family:"Arial Unicode MS"">3503 RM Utrecht</span></div></div></div><div style="font-size:14px"><br></div></font></div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><span style="color:rgb(72,72,72);font-family:"Arial Unicode MS";font-size:12px">E-mail:</span><span style="color:rgb(72,72,72);font-family:"Arial Unicode MS";font-size:12px"> </span><a href="mailto:femke.francissen@biosb.nl" style="font-family:"Arial Unicode MS";font-size:12px;color:rgb(17,85,204)" target="_blank">femke.francissen@<wbr>biosb.nl</a><span style="color:rgb(72,72,72);font-family:"Arial Unicode MS";font-size:12px"> </span></div><div style="color:rgb(0,0,0);font-family:Calibri,sans-serif;word-wrap:break-word"><font face="Arial Unicode MS" color="#484848"><div style="font-size:14px"><span style="font-size:12px">Mobile: +31 6 17 90 4888</span></div><div style="font-size:14px"><span style="font-size:12px">Skype: femke.francissen</span><br></div><div style="font-size:14px"><span style="font-size:12px">Website: </span><span style="font-size:12px"><font color="#800080"><a href="http://www.biosb.nl/" target="_blank">www.biosb.nl</a></font></span><span style="font-size:12px"><br></span></div></font></div><div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;word-wrap:break-word"><font style="color:rgb(0,0,0);font-family:Calibri,sans-serif;font-size:14px"><span style="font-size:12px">LinkedIn <a href="http://nl.linkedin.com/in/femkefrancissen" style="color:rgb(17,85,204)" target="_blank">link</a></span></font></div><div style="color:rgb(34,34,34);font-family:arial,sans-serif;font-size:small;word-wrap:break-word"><br></div><div style="word-wrap:break-word"><img src="http://www.dtls.nl/wp-content/uploads/2014/09/BioSB_logo_full_250x226.jpg" width="96" height="85"><br></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div></div>
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