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<p class="MsoNormal"><span lang="NL-BE">Dear,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">I have read the manuscript on the MAKER-P tool. I’m finishing the last part of my plant genome assembly and MAKER-P will be used for determine gene annotations. I have read the wiki tutorials and your manuscript but one
thing comes to my mind on evidence sources when RNAseq data is available for gene discovery (like we have). :<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">Why do you perform a RNA denovo assembly with individual RNAseq runs. As I could understand from your paper (a tool kit for the raped creation,…), the RNAseq reads were short single reads. This includes that it is not
easy for denovo RNA assemblers (like trinity) to find high quality genes since a lot of reads will be lost because of the low coverage. If 2*200 PE reads were used for RNAseq, this would create more genes.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">Therefore, as an alternative: why not mapping the RNAseq reads to your reference genome. Extract this as a fasta file and cutoff all the reads shorter than 150 bp long. If you concentate all the RNAseq data to one file
before the mapping, all your expressed RNA is mapped and included in the fasta file that you need for gene discovery.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">From my opinion, the low-expressed reads will be lost during the assembly. Or am I overlooking something?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">We have sequenced our genome with PE illumina data. For DE analyses, we did run 48 single reads 50 bp , lower coverage.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">Therefore, is assembling the RNAseq data still better than mapping the data to our reference genome?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">PS: can I add a question on the google group? I couldn’t start a new topic<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">Thanks in advance,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL-BE">Arne Van Hoeck<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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