<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div style="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><span style="font-family: Menlo; font-size: 11px;"><br></span></div><div style="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); 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="color: rgb(0, 0, 0); font-family: Calibri, sans-serif; font-size: 14px;"><div style="font-family:Calibri; font-size:11pt; text-align:left; color:black; BORDER-BOTTOM: medium none; BORDER-LEFT: medium none; PADDING-BOTTOM: 0in; PADDING-LEFT: 0in; PADDING-RIGHT: 0in; BORDER-TOP: #b5c4df 1pt solid; BORDER-RIGHT: medium none; PADDING-TOP: 3pt"><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></body></html>