<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Carson,<div><br></div><div><div><div>Given that I now have maker transcripts, ab initio predicted transcripts and transcripts that don’t overlap, which ones are reflected in the gff file?</div><div><br></div><div>The ids in the gff file (for exons, genes, mrna) all say something like ‘*snap-gene’ so does this mean these are the genes from the snap prediction tool?</div><div><br></div><div><br></div><div>Thanks</div><div>dhivya</div><div><br></div><div><br></div><div><br></div><div>On Mar 18, 2014, at 3:09 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div><font face="Consolas">There can also be hint based predictions. They may be similar in size, but there is no rule. Generally <span style="font-size: 11px;">maker.snap_masked.proteins.fasta will be larger, as gene predictors tend to </span><font size="2">over predict (as much as 10 fold). You should always review your annotations in something like Apollo, to see how the models compare to the evidence. Just counts don’t really mean anything.</font></font></div><div><font size="2" face="Consolas"><br></font></div><div><font size="2" face="Consolas">Thanks,</font></div><div><font size="2" face="Consolas">Carson</font></div><div style="font-family: Calibri, sans-serif; font-size: 14px;"><br></div><span id="OLK_SRC_BODY_SECTION" style="font-family: Calibri, sans-serif; font-size: 14px;"><div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);"><span style="font-weight:bold">From: </span> dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, March 18, 2014 at 2:05 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> Re: maker snap output files<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Thanks Carson.<div><br></div><div>Is it normal that in my maker results after running snap, the number of proteins (in *<span style="font-family: Menlo; font-size: 11px;">maker.proteins.fasta) </span>Is actually less than the number of proteins in my pre-snap maker results? I assumed that annotations through alignment+annotation through prediction would equal more annotations?</div><div><br></div><div>The unfiltered proteins file has more proteins though.</div><div><br></div><div>Thanks</div><div>Dhivya</div><div><br></div><div><br></div><div><br></div><div><div>On Mar 18, 2014, at 2:34 PM, Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="font-family: Calibri, sans-serif; font-size: 14px;"><span style="font-family: Menlo; font-size: 11px;">maker.proteins.fasta - these are the final filtered and modified protein models (this is what you want)</span></div><div style="font-family: Calibri, sans-serif; font-size: 14px;"><span style="font-family: Menlo; font-size: 11px;">maker.snap_masked.proteins.fasta - these are the raw unfiltered snap ab initio predictions (for reference purposes)</span></div><div><span style="font-family: Menlo; font-size: 11px;">maker.non_overlapping_ab_initio.proteins.fasta - these are non-redundant rejected models that do not overlap the </span><font face="Menlo" size="2">maker.proteins.fasta entries. If you think you are missing a gene, look for it here. Sometimes people use interproscan (very slow) to analyze this file for false negatives.</font></div><div style="font-family: Calibri, sans-serif; font-size: 14px;"><span style="font-family: Menlo; font-size: 11px;"><br></span></div><div style="font-family: Calibri, sans-serif; font-size: 14px;"><span style="font-family: Menlo; font-size: 11px;"><br></span></div><div><font face="Menlo" size="2">These files are also described in the README distributed with MAKER in the “MAKER OUTPUT” section.</font></div><div><font face="Menlo" size="2"><br></font></div><div><font face="Menlo" size="2">Thanks,</font></div><div><font face="Menlo" size="2">Carson</font></div><div><font face="Menlo" size="2"><br></font></div><div><font face="Menlo" size="2"><br></font></div><div><font face="Menlo" size="2"><br></font></div><div style="font-family: Calibri, sans-serif; font-size: 14px;"><span style="font-family: Menlo; font-size: 11px;"><br></span></div><span id="OLK_SRC_BODY_SECTION" style="font-family: Calibri, sans-serif; font-size: 14px;"><div style="font-family: Calibri; font-size: 11pt; text-align: left; border-width: 1pt medium medium; border-style: solid none none; padding: 3pt 0in 0in; border-top-color: rgb(181, 196, 223);"><span style="font-weight:bold">From: </span> dhivya arasappan <<a href="mailto:darasappan@gmail.com">darasappan@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, March 18, 2014 at 1:27 PM<br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com">carsonhh@gmail.com</a>>, <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> maker snap output files<br></div><div><br></div><div><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hello,<div><br></div><div>I ran maker after running SNAP ab initio prediction (following instructions from the maker tutorial). It ran successfully and when I ran fasta_merge, I got several output fasta files. I’m unable to find information on the tutorial about interpreting these different files. I’m hoping one of you can help.</div><div><br></div><div>*<span style="font-family: Menlo; font-size: 11px;">maker.proteins.fasta</span></div><div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">*maker.snap_masked.proteins.fasta</div></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">*maker.non_overlapping_ab_initio.proteins.fasta</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">What is the difference among these? They all have different number of sequences.</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;">Similarly,with transcripts:</div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><div style="margin: 0px;">maker.non_overlapping_ab_initio.transcripts.fasta</div><div style="margin: 0px;"><div style="margin: 0px;">maker.snap_masked.transcripts.fasta</div><div style="margin: 0px;"><div style="margin: 0px;">maker.transcripts.fasta</div><div style="margin: 0px;"><br></div><div style="margin: 0px;">Thanks</div><div style="margin: 0px;">Dhivya</div><div style="margin: 0px;"><br></div></div></div></div><div style="margin: 0px; font-size: 11px; font-family: Menlo;"><br></div></div></div></span></div></blockquote></div><br></div></div></span></div>
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