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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Exactly<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">chris<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black">Carson Holt <carsonhh@gmail.com><br>
<b>Date: </b>Tuesday, January 31, 2017 at 3:35 PM<br>
<b>To: </b>Quanwei Zhang <qwzhang0601@gmail.com><br>
<b>Cc: </b>Chris Fields <cjfields@illinois.edu>, "maker-devel@yandell-lab.org" <maker-devel@yandell-lab.org><br>
<b>Subject: </b>Re: [maker-devel] Transcript assembly of RNA-seq data from different tissues and individuals<o:p></o:p></span></p>
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<p class="MsoNormal">I think he means not to combine them for the transcript assembly preparation (i.e. assembly them separately). But you still provide them all to maker as a comma separated list.
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<p class="MsoNormal">—Carson<o:p></o:p></p>
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<p class="MsoNormal">On Jan 31, 2017, at 2:33 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com">qwzhang0601@gmail.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Thank you guys for your suggestions. So you do not suggest to use RNA-seq data from another study, even I assemble them separately and then provide both assemblies into Maker as a comma separated list. The issues
you mentioned do exist, but some people did collect RNA-seq data from different individuals and used them for gene annotation (e.g., doi:10.1038/ng.3198). But thank you for your suggestions, I will think about it.<o:p></o:p></p>
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<p class="MsoNormal">Best<o:p></o:p></p>
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<p class="MsoNormal">Quanwei <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">2017-01-31 16:05 GMT-05:00 Fields, Christopher J <<a href="mailto:cjfields@illinois.edu" target="_blank">cjfields@illinois.edu</a>>:<o:p></o:p></p>
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<p class="MsoNormal">I agree with Mike. I also suggest not combining RNA-Seqs from different runs (e.g. different studies) even if they are from the same tissue, development stage etc. There are many other factors (biological variation, sample quality, sequencing
chemistry or technology differences, etc) that can significantly and negatively impact trx assembly quality.<br>
<br>
chris<o:p></o:p></p>
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On 1/31/17, 1:26 PM, "maker-devel on behalf of Michael Campbell" <<a href="mailto:maker-devel-bounces@yandell-lab.org">maker-devel-bounces@yandell-lab.org</a> on behalf of
<a href="mailto:michael.s.campbell1@gmail.com">michael.s.campbell1@gmail.com</a>> wrote:<br>
<br>
I would probably try merging the replicates but not the tissues. You can then pass the output files to MAKER in a comma separated list in the opts file.<br>
<br>
Example:<br>
est=/PATH/TO/file1.fsata,/PATH/TO/file2.fasta<br>
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Good luck,<br>
Mike<br>
<br>
> On Jan 31, 2017, at 2:08 PM, Quanwei Zhang <<a href="mailto:qwzhang0601@gmail.com">qwzhang0601@gmail.com</a>> wrote:<br>
><br>
> Hello:<br>
><br>
> I am trying to assemble transcripts using RNA-seq data by the tool Trinity, which will be used for gene annotation for Maker. Now I have data from two tissues with two replicates each. Should I merge all four samples to get one assembly file? Or should
I merge replicates of each tissue separately and use the two assembly files as input of Maker. Merging all samples into one, we will have much higher coverage level, but I think there may be some genes expressed by tissue-specific isoforms. So I not sure whether
I should merge RNA-seq from different tissues.<br>
> What's more, I find some published RNA-seq data from another individual (and also for different tissue from us) for the same species. Should I merge all RNA-seq together (across individuals and tissues)? Or should I generate different transcript assembly
and use all those assemblies as input to Maker?<br>
><br>
> Thanks<br>
> Best<br>
> Quanwei<br>
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