<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>Dear Joann,</div><div><br></div><div>I'm not Dr Brown, but we also do a lot of RNAseq on plants, so perhaps I can offer out experience.</div><div><br></div><div>We use either RSEM or eXpress for quantification. The results are almost identical from the two, but eXpress is much faster while RSEM allows you to extract the probabilities for each alignment, so they are each useful in different scenarios. We tend to use Bowtie1 for quantification.</div><div><br>Richard Smith</div><div>Department of Plant Sciences</div><div>University of Cambridge</div><div><br>On 17 Sep 2013, at 23:54, Joann Diray Arce <<a href="mailto:joann.diray@gmail.com">joann.diray@gmail.com</a>> wrote:<br><br></div><blockquote type="cite"><div><div dir="ltr">Dr. Brown,<div><br></div><div><div><font face="arial, helvetica, sans-serif">I am doing RNA-seq with plants. Do you have any preferred aligner and software that will do abundance estimation?</font></div><div>
<font face="arial, helvetica, sans-serif"><br></font></div><div style=""><font face="arial, helvetica, sans-serif">-Joann Arce</font></div>
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