[maker-devel] interpreting SNAP gene-stats output

[Carson Holt]

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.

--Carson


From:  Sally Chang <eschang1 at gmail.com>
Date:  Tuesday, September 30, 2014 at 2:02 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] interpreting SNAP gene-stats output

Hi all,
I was wondering if someone could help me make sure I am looking at these
results from running fathom -gene-stats on an annotation:

1049 sequences
0.245825 avg GC fraction (min=0.162446 max=0.431287)
5533 genes (plus=2760 minus=2773)
91 (0.016447) single-exon
5442 (0.983553) multi-exon
101.857010 mean exon (min=1 max=6534)
81.880493 mean intron (min=4 max=5486)

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?).

Thanks very much,
Sally Chang

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