<div dir="ltr">Hi Julian,<div><br></div><div>Since you are annotating a primate I would use the pre-trained human parameter for augustus. Here is what I would try first</div><div><br></div><div> <span style="font-size:13px;color:rgb(0,0,0);font-family:Tahoma">genome=data/hsap_contig.fasta </span><span style="font-size:13px;color:rgb(0,0,0);font-family:Tahoma"> # contig file from example data</span></div><span style="color:rgb(0,0,0);font-family:Tahoma;font-size:13px">est=data/mRNAs.fa # RNAs filtered to just mRNAs</span><br style="color:rgb(0,0,0);font-family:Tahoma;font-size:13px"><span style="color:rgb(0,0,0);font-family:Tahoma;font-size:13px">protein=data/protein.fa</span><br style="color:rgb(0,0,0);font-family:Tahoma;font-size:13px"><span style="color:rgb(0,0,0);font-family:Tahoma;font-size:13px">est2genome=0</span><br style="color:rgb(0,0,0);font-family:Tahoma;font-size:13px"><span style="color:rgb(0,0,0);font-family:Tahoma;font-size:13px">protein2genome=0</span><div><span style="color:rgb(0,0,0);font-family:Tahoma">augustus_species=human</span><br></div><div><font color="#000000" face="Tahoma"><br></font></div><div><font color="#000000" face="Tahoma">You could also use one of the mammal HMMs packaged with SNAP as well, or use the output from the above to train SNAP. There are tutorial that walk through these steps here: </font></div><div><font color="#000000" face="Tahoma"><br></font></div><div><font color="#000000" face="Tahoma"><a href="http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page">http://weatherby.genetics.utah.edu/MAKER/wiki/index.php/Main_Page</a></font></div><div><font color="#000000" face="Tahoma"><br></font></div><div><font color="#000000" face="Tahoma">There is also a current protocols in bioinformatics article for using MAKER can may help you get started as well.</font></div><div><font color="#000000" face="Tahoma"><br></font></div><div><font color="#000000" face="Tahoma"><a href="http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0411s48/abstract">http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0411s48/abstract</a><br></font></div><div><font color="#000000" face="Tahoma"><br></font></div><div><font color="#000000" face="Tahoma">Good luck,</font></div><div><font color="#000000" face="Tahoma">Mike</font></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, May 19, 2015 at 1:51 PM, Julian Egger <span dir="ltr"><<a href="mailto:julian.egger@omahazoo.com" target="_blank">julian.egger@omahazoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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I am trying to use Augustus in MAKER to help with annotating as many genes as possible from genomic reads of a primate sample. I am new to using gene prediction tools such as SNAP and Augustus, but was told Augustus would be better for primates. I tried using
reference mRNAs and protein sequences from NCBI on the sample contig file included with the MAKER software and it ran ok. My question is how do I now use the output to train Augustus iteratively and thus create a file set of annotations from my original input?
<br>
<br>
After creating the control files with maker -CTL, the only configurations I made to maker_opts.ctl were:<br>
genome=data/hsap_contig.fasta # contig file from example data<br>
est=data/mRNAs.fa # RNAs filtered to just mRNAs<br>
protein=data/protein.fa<br>
est2genome=1<br>
protein2genome=1<br>
<br>
I will eventually replace the contig file with our scaffolds file from the assembly. I know the output created a gff file along with protein and mRNA files. Do I then need to change the maker_opts file to account for the new files and if so how and what should
the maker__opts file look like now? Was Augustus supposed to be set up on the initial maker run or do I wait until the second run after est2genome and protein2genome were used to initialize training for Augustus and how do the configurations change between
multiple iterations because I have a solid annotation set? <br>
<br>
Sorry for all the questions, newbie here with a lot of data to work with. <br>
<br>
Thanks<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">Michael Campbell MS, RD.<br>Doctoral Candidate<br>Eccles Institute of Human Genetics<br>
University of Utah<br>
15 North 2030 East, Room 2100<br>
Salt Lake City, UT 84112-5330<br>ph:585-3543<br><br></div></div>
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