<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; color: rgb(0, 0, 0); font-size: 14px; font-family: Calibri, sans-serif;"><div>Probably. But it's really not that important of a value because during the 'fathom -genome.ann genome.dna -categorize 1000' step outlined in the SNAP training literature, fathom turns each gene into it's own little contig padded by 1000bp on either size. So in the end the number of starting contigs becomes irrelevant, because they all get trimmed and thrown away anyways.</div><div><br></div><div>--Carson</div><div><br></div><div><br></div><span id="OLK_SRC_BODY_SECTION"><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> Sally Chang <<a href="mailto:eschang1@gmail.com">eschang1@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Tuesday, September 30, 2014 at 2:02 PM<br><span style="font-weight:bold">To: </span> <<a href="mailto:maker-devel@yandell-lab.org">maker-devel@yandell-lab.org</a>><br><span style="font-weight:bold">Subject: </span> [maker-devel] interpreting SNAP gene-stats output<br></div><div><br></div><div dir="ltr">Hi all,<br>I was wondering if someone could help me make sure I am looking at these results from running fathom -gene-stats on an annotation: <br><div><br>1049 sequences<br>0.245825 avg GC fraction (min=0.162446 max=0.431287)<br>5533 genes (plus=2760 minus=2773)<br>91 (0.016447) single-exon<br>5442 (0.983553) multi-exon<br>101.857010 mean exon (min=1 max=6534)<br>81.880493 mean intron (min=4 max=5486)<br><br></div><div>Are the 1049 sequences the actual number of contigs/sequences from your assembly that MAKER ended up using? And is that 5533 genes the number of genes it found on those contigs (and strand info?). <br><br></div><div>Thanks very much,<br></div><div>Sally Chang<br></div><div><br></div></div>
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