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<p>Hi Carson,</p>
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<p>If I want to look for alternative splicing variant, can I just add the option </p>
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<p>alt_splice=1</p>
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<p>only at the last round of maker or do I have to set it since the beggining ? (and perform the 4 rounds with this option).<br>
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Cheers,</div>
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Patrick<br>
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<div id="divRplyFwdMsg" dir="ltr"><font style="font-size:11pt" face="Calibri, sans-serif" color="#000000"><b>From:</b> Carson Holt <carsonhh@gmail.com><br>
<b>Sent:</b> Friday, September 22, 2017 10:08 PM<br>
<b>To:</b> Patrick Tran Van<br>
<b>Cc:</b> maker-devel@yandell-lab.org<br>
<b>Subject:</b> Re: [maker-devel] Advice on my pipeline</font>
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<div>The gff3 passthrough options are there to help users get old data into MAKER when they have lost access to the original files. But for iterative running of the pipeline, it is more effective just to rerun in place so MAKER can access the raw alignment
reports. The raw reports from the alignments have more detail than what is stored in the GFF3. Details that are lost when trying to use the GFF3 as input.
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<div class="">—Carson<br class="">
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<div class="">On Sep 21, 2017, at 3:26 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div>
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<span class="" style="font-family:'Courier New',monospace"><span class="" style="font-family:'Times New Roman',Times,serif">Hi Carson,</span><br class="">
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<span class="" style="font-family:'Courier New',monospace"></span>I have a doubt for the round 2, so in a previous reply you said:</div>
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" Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option is really more
for getting data into the run from jobs performed a long time ago (so they can’t be run in the same directory). "<br class="">
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Does it means that I don't need to modify the section :</div>
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#-----Re-annotation Using MAKER Derived GFF3</div>
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?</div>
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If I let everything by default such as :</div>
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altest_pass=0 #use alternate organism ESTs in maker_gff: 1 = yes, 0 = no<br class="">
protein_pass=0 #use protein alignments in maker_gff: 1 = yes, 0 = no<br class="">
rm_pass=0 #use repeats in maker_gff: 1 = yes, 0 = no<span class="Apple-converted-space"> </span><br class="">
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It will not look again for repeat and protein + transcriptome alignment ?<br class="">
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<br class="">
Patrick Tran Van<br class="">
<br class="">
Groups Chapuisat, Robinson-Rechavi & Schwander<br class="">
Department of Ecology and Evolution<br class="">
University of Lausanne<br class="">
Le Biophore<br class="">
CH-1015 Lausanne<br class="">
Switzerland<br class="">
Office 3206<br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font class="" style="font-size:11pt" face="Calibri, sans-serif"><b class="">From:</b><span class="Apple-converted-space"> </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, July 3, 2017 10:50 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Patrick Tran Van<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] Advice on my pipeline</font>
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<div class="">maker2zff is just for SNAP training and not for gene filtering (please do not use it for filtering, it does not do what you think).
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<div class="">So the final annotation set after maker with correct_est_fusion is 16,850. To decide which set is better, look at them in a browser (gene counts are not useful for guaging result). A well annotated genome will have evidence clusters that closely
match the final models. A poorly annoted genome will have evidence clusters that are split or merged by the models.</div>
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<div class="">The corrected_est_fusion does two things. It trims long overlapping UTR fragments, and it stops evidence clusters from being merged on BLASTP evidence alone (so gene predictors will get unmerged hint regions if clusters are split).</div>
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<div class="">You may also find that using jaccard_clip with Trinity has reduced sensitivity for the transcript data (you may lose things that were there before, but now have better specificity, i.e. fewer false positives). Make sure you provided protein data
from at least two related species to help maintain sensitivity lost form the transcript data. You can also add rejected genes models back in after the fact by using iprscan to identify unsupported models with identifiable protein domains —> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/" class="">https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286374/</a></div>
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<div class="">Thanks,</div>
<div class="">Carson</div>
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<div class="">On Jul 1, 2017, at 5:21 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div>
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I have assembled my transcriptome with Trinity using the jaccard clip option and I have run maker with and without corrected_est_fusion.</span>
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I have then use SNAP to train/filter it with:</div>
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maker2zff specie.all.gff</div>
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Here are my results:</div>
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Number of gene after maker -> Number of gene after maker2zff</div>
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- Without corrected_est_fusion: 21621 -> 13875</div>
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- With corrected_est_fusion: 16850 -> 9098</div>
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1 )If I understand well how works corrected_est_fusion, because it prevents gene merging, shouldn't be the invert ?</div>
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Normally I should find more genes with corrected_est_fusion right ?</div>
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2) I think I should find something like 13000-14000 genes for my specie. SHould I go with the "Without corrected_est_fusion" for the 2nd iteration of maker ?</div>
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Thanks for your help<span class="Apple-converted-space"> </span><br class="">
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<br class="">
Patrick Tran Van<br class="">
<br class="">
Groups Chapuisat, Robinson-Rechavi & Schwander<br class="">
Department of Ecology and Evolution<br class="">
University of Lausanne<br class="">
Le Biophore<br class="">
CH-1015 Lausanne<br class="">
Switzerland<br class="">
Office 3206<br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font class="" style="font-size:11pt" face="Calibri, sans-serif"><b class="">From:</b><span class="Apple-converted-space"> </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, June 26, 2017 11:38 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Patrick Tran Van<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] Advice on my pipeline</font>
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<div class="">Sorry the option is —> correct_est_fusion
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<div class="">It is in the maker_opts.ctl file.</div>
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<div class="">I would use both SNAP and Augustus on a few large contigs then review the results manually. If one of them is not behaving well, then drop it. If both behave well (i.e. correlate well with evidence alignemnts) then keep them both.</div>
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<div class="">—Carson</div>
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<div class="">On Jun 26, 2017, at 3:48 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div>
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Thanks for your answer.</div>
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1) Do you think that adding a Augustus training in addition to SNAP at the step 3 and 5 will add more confidence (instead of adding Augustus only for the final round) ?</div>
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Because I am using autoAug for this and it tooks a while to compute ..</div>
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2) I don't see this option : 'avoid_est_fusion=1' . I have tried to add it but I got this error:</div>
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WARNING: Invalid option 'avoid_est_fusion' in control file maker_opts.ctl</div>
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(I am using v 2.31.8 )<br class="">
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<br class="">
Patrick Tran Van<br class="">
<br class="">
Groups Chapuisat, Robinson-Rechavi & Schwander<br class="">
Department of Ecology and Evolution<br class="">
University of Lausanne<br class="">
Le Biophore<br class="">
CH-1015 Lausanne<br class="">
Switzerland<br class="">
Office 3206<br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font class="" style="font-size:11pt" face="Calibri, sans-serif"><b class="">From:</b><span class="Apple-converted-space"> </span>Carson Holt <<a href="mailto:carsonhh@gmail.com" class="">carsonhh@gmail.com</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, June 5, 2017 8:29 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Patrick Tran Van<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:maker-devel@yandell-lab.org" class="">maker-devel@yandell-lab.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [maker-devel] Advice on my pipeline</font>
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<div class="">Your plan sounds good. A couple of related notes.
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<div class="">Insect genomes tend to have high gene density, so gene merging will be the primary difficulty. You can avoid merging of mRNA-seq evidence by using options like jaccard_clip in Trinity. Then use avoid_est_fusion=1 inside of MAKER.</div>
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<div class="">Also it is more convenient to do each run in the same directory rather than supplying the previous run as GFF3 input. MAKER will automatically recycle previous results archived in the run directory when you do this. Using the maker_gff option
is really more for getting data into the run from jobs performed a long time ago (so they can’t be run in the same directory).</div>
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<div class="">—Carson</div>
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<blockquote type="cite" class="">
<div class="">On Jun 2, 2017, at 3:56 AM, Patrick Tran Van <<a href="mailto:Patrick.TranVan@unil.ch" class="">Patrick.TranVan@unil.ch</a>> wrote:</div>
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Hello,<br class="">
<br class="">
This is my first time running Maker for an insect genome annotation.<span class="Apple-converted-space"> </span><br class="">
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I have found various resources and tried to make a consensus, I am looking for your thoughts and advices about my pipeline, if I can improve something or doing useless things:<br class="">
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What I have:<br class="">
- RNA evidence: transcriptome<br class="">
- Proteine evidence: swissprot/uniprot + busco protein set of insect<br class="">
- Cegma and busco results of my genome<br class="">
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<br class="">
1) Train SNAP with CEGMA<br class="">
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2) Run (run A) maker with repeat masking with transcript, protein, the new SNAP file (from step 1) and augustus file (from busco).<br class="">
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3) Create SNAP model from run A.<br class="">
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4) Run (run B ) with the new SNAP (done at step 3) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_A.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).<br class="">
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5) Create SNAP model from run B.<br class="">
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6) Run (run C) with the new SNAP (done at step 5) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_B.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1 and protein_pass=1).<br class="">
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7) Create SNAP model from run C AND Create Augustus gene model from run C<br class="">
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8) Run (run D) with the new SNAP (done at step 7) + AUGUSTUS file (step 7) with options turned off (est2genome=0) and (protein2genome=0) data, provide gff file (maker_gff=run_C.gff), turn off repeat masking (rm_pass=1), and use previous mapping results (altest_pass=1
and protein_pass=1). + Use keep_preds=1<br class="">
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Does it seems coherent ?</div>
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Cheers,<br class="">
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<div name="divtagdefaultwrapper" class="" style="font-family:Calibri,Arial,Helvetica,sans-serif; margin:0px">
<br class="">
Patrick Tran Van<br class="">
<br class="">
Groups Chapuisat, Robinson-Rechavi & Schwander<br class="">
Department of Ecology and Evolution<br class="">
University of Lausanne<br class="">
Le Biophore<br class="">
CH-1015 Lausanne<br class="">
Switzerland<br class="">
Office 3206<br class="">
<br class="">
</div>
</div>
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