<div dir="ltr"><div><font color="#000000">Hi Titus,</font></div><div><font color="#000000"><br></font></div><div><font color="#000000">Im trying to do a consensus transcriptome from fourteen transcriptomic</font></div><div>
<font color="#000000">libraries.</font></div><div><font color="#000000"><br></font></div><div><font color="#000000">For this end, I join all the reads of the 14 libraries, and then run Diginorm</font></div><div><font color="#000000">and Trinity in silico normalization (Trinitynorm) before the assembly (with Trinity). </font></div>
<div><font color="#000000">I also did the assembly using the join of all 14 libraries reads without any </font></div><div><font color="#000000">normalization ("multireads strategy"). </font></div><div><font color="#000000"><br>
</font></div><div><font color="#000000">Unexpectedly, the multireads strategy was the best reconstructing the</font></div><div><font color="#000000">coding sequences. I think that this is given by the fact that the assembly from multireads </font></div>
<div><font color="#000000">assembled longest contigs (despite that the contig median and average length is lower </font></div><div><font color="#000000">compared with the assembly from both normalization algorithms)</font></div>
<div><font color="#000000"><br></font></div><div><font color="#000000">On the other hand, it seems that the assembly from normalization</font></div><div><font color="#000000">algorithms "recovered" more (potentially) isoforms.</font></div>
<div><font color="#000000">If I look for the number of contigs that were reconstructed for each</font></div><div><font color="#000000">coding sequence, normalization strategies reconstructed more contigs</font></div><div>
<font color="#000000">than multireads (despite normalization strategy reconstructs worse the</font></div><div><font color="#000000">distinct coding sequences). --Please see the attached file.— In fact I</font></div><div>
<font color="#000000">calculated the average number of repeated "comp_XXX" (using the ID of</font></div>
<div><font color="#000000">Trinity assembled contigs, that I think, are alternatives</font></div><div><font color="#000000">reconstructions of a given contig) and Diginorm and Trinitynorm</font></div><div><font color="#000000">assembly had the double that the assembly from multireads.</font></div>
<div><font color="#000000"><br></font></div><div><font color="#000000">Other thing that I saw, is that the assembly after normalizations</font></div><div><font color="#000000">recovered more distinct genes in total (after blastx annotation).</font></div>
<div><font color="#000000"><br></font></div><div><font color="#000000">Do you think that my explanations of the results are fine? Any idea on</font></div><div><font color="#000000">why the assembly after normalization cause a more fragmented assembly?</font></div>
<div><font face="arial, helvetica, sans-serif" color="#000000">(I ran both, Diginorm and Trinitynorm with a "K" (kmer) of 25 )</font></div><div><font face="arial, helvetica, sans-serif" color="#000000"><br></font></div>
<div><font face="arial, helvetica, sans-serif" color="#000000">*Diginorm command: </font></div><div><font face="arial, helvetica, sans-serif" color="#000000">normalize-by-median.py -p -C 30 -k 25 -N 4 -x 2.5e9 reads_shuffled.fastq</font></div>
<div><font face="arial, helvetica, sans-serif" color="#000000"><br></font></div><div><font face="arial, helvetica, sans-serif" color="#000000">*Trinitynorm command:</font></div><div><pre style="padding:0px;margin-top:0px;margin-bottom:0px">
<tt><font face="arial, helvetica, sans-serif" color="#000000"><a href="http://normalize_by_kmer_coverage.pl">normalize_by_kmer_coverage.pl</a> --seqType fq --JM 100G --max_cov 30 --left left.fq --right right.fq --pairs_together --PARALLEL_STATS --JELLY_CPU 10</font></tt></pre>
</div><div><font color="#000000"><br></font></div><div><font color="#000000">The assembly was performed using paired end reads. For run Diginorm, I</font></div><div><font color="#000000">shuffle the reads before the normalization.</font></div>
<div><font color="#000000"><br></font></div><div><font color="#000000">Thanks in advance and sorry for the bad english,</font></div><div><font color="#000000"><br></font></div><div><font color="#000000">Facundo </font></div>
<div><br></div>-- <br><div><p style="text-align:left;margin-bottom:0cm"><span style="font-family:Verdana,sans-serif"><a href="http://oilcrash.net/recursos/promptuarium/prontuario/" target="_blank"><font color="#000000"><span style="font-style:normal"><b>The
Oil Crash</b></span></font></a></span></p><p style="margin-bottom:0cm;text-align:left"><font face="Verdana, sans-serif"><font><b>
</b></font></font></p><p style="text-align:left;font-size:4pt;margin-bottom:0.5cm;font-style:normal"><font face="Verdana, sans-serif"><font><b>
<font color="#333333"><font face="Verdana, sans-serif"><font size="1" style="font-size:6pt">La
Urgente Necesidad de Cobrar Consciencia</font></font></font></b></font></font></p><font face="Verdana, sans-serif"><font>
<p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><a href="http://www.theeestory.com/files/PeakOil.pdf" target="_blank"><font color="#333333"><font face="Verdana, sans-serif"><font size="1" style="font-size:6pt"><span style="font-style:normal"><b>Peak
Oil Production May Already Be Here. Science 2011</b></span></font></font></font></a></p>
<p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><a href="http://wendang.baidu.com/view/d30f4cfc04a1b0717fd5dde0.html" target="_blank"><font color="#333333"><font face="Verdana, sans-serif"><font size="1" style="font-size:6pt"><span style="font-style:normal"><span style="font-weight:normal">That's
oil, folks. Nature 2007</span></span></font></font></font></a></p>
<p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><a href="http://www.tsl.uu.se/uhdsg/publications/peakoilage.pdf" target="_blank"><font color="#333333"><font face="Verdana, sans-serif"><font size="1" style="font-size:6pt"><span style="font-style:normal"><b>The
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<p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><a href="http://www.qeh.ox.ac.uk/pdf/pdf-research/Global%20Energy%20Crunch.pdf" target="_blank"><font color="#333333"><font face="Verdana, sans-serif"><font size="1" style="font-size:6pt"><span style="font-style:normal"><span style="font-weight:normal">Global
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<p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><br>
</p>
</font></font><p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><font face="Verdana, sans-serif"><font><font color="#333333"><font face="Verdana, sans-serif"><font size="1" style="font-size:6pt"><span style="font-style:normal"><a href="http://www.worldenergyoutlook.org/docs/weo2010/weo2010_es_spanish.pdf" style="font-weight:normal" target="_blank"><font color="#333333">IEA</font></a>-<a href="http://www.imf.org/external/pubs/ft/weo/2011/01/pdf/text.pdf" target="_blank"><font color="#333333"><b>FMI</b></font></a>-<font color="#333333"><font color="#333333"><a href="http://www.lloyds.com/~/media/Lloyds/Reports/360%20Energy%20Security/7238_Lloyds_360_Energy_Pages.pdf" target="_blank"><font color="#333333">Chatham House</font></a></font>-<a href="http://www.energywatchgroup.org/fileadmin/global/pdf/2008-02_EWG_Oil_Report_updated.pdf" target="_blank"><font color="#333333"><b>EWG</b></font></a>-<a href="http://peakoiltaskforce.net/download-the-report/2010-peak-oil-report/" style="font-weight:normal" target="_blank"><font color="#333333">ITPOES</font></a></font>-<b>JFCOM</b>-<a href="http://peak-oil.com/download/Peak%20Oil.%20Sicherheitspolitische%20Implikationen%20knapper%20Ressourcen%2011082010.pdf" style="font-weight:normal" target="_blank"><font color="#333333">Bundeswehr</font></a>-<a href="http://green.blogs.nytimes.com/2011/03/08/a-dark-warning-on-global-oil-demand/" target="_blank"><font color="#333333"><b>Hess
Corporation</b></font></a></span></font></font></font></font></font></p>
<p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><font color="#333333"><font face="Verdana, sans-serif"><font size="1" style="font-size:6pt"><span style="font-style:normal"><a href="http://www.nytimes.com/2010/12/27/opinion/27krugman.html" target="_blank"><font color="#333333"><b>Paul
Krugman</b></font></a>-<a href="http://www.crisisenergetica.org/article.php?story=20110408153709150" style="font-weight:normal" target="_blank"><font color="#333333">François
Fillon</font></a>-<a href="http://www.crisisenergetica.org/article.php?story=20101015205730248" target="_blank"><font color="#333333"><b>Robert
Hirsch</b></font></a></span></font></font></font></p>
<p align="LEFT" style="font-size:4pt;margin-bottom:0cm"><br></p><p></p></div>
</div>