Problems with understanding Quake's outputs

zlix425 · 07-17-2011, 10:09 PM

Hi, I am new to this area and I am currently working on Illumina GA data analysis. I have this output from the software Quake:

...3598636 sequences processed, 359863600 bp scanned
WARNING: Input had 352880 non-DNA (ACGT) characters whose kmers were not counted
11120988 total distinct mers
11120988 mers occur at least 0 times
initial value 63013.294557
iter 10 value 57511.692087
iter 20 value 56339.034500
iter 30 value 56016.040353
iter 40 value 56012.926228
iter 50 value 56011.300715
final value 56010.011528
converged
value: 56010.01
$zp.copy
[1] 3.078884

$p.e
[1] 0.715543

$shape.e
[1] 0.1971554

$scale.e
[1] 1.328558

$u.v
[1] 57.375

$var.v
[1] 880.9596

I am not sure if the "warning" produced above affects the results? Also, I am not quite sure what are the meanings of "iter" values above as I could not find the meaning of these terms from the literature.

Thanks for anyone that could help.

ECO · 07-17-2011, 10:21 PM

Don't crosspost. Your other post was deleted. One post, one location.

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07-17-2011, 10:09 PM	#1
zlix425 Junior Member Location: Australia Join Date: Jul 2011 Posts: 1	Problems with understanding Quake's outputs Hi, I am new to this area and I am currently working on Illumina GA data analysis. I have this output from the software Quake: ...3598636 sequences processed, 359863600 bp scanned WARNING: Input had 352880 non-DNA (ACGT) characters whose kmers were not counted 11120988 total distinct mers 11120988 mers occur at least 0 times initial value 63013.294557 iter 10 value 57511.692087 iter 20 value 56339.034500 iter 30 value 56016.040353 iter 40 value 56012.926228 iter 50 value 56011.300715 final value 56010.011528 converged value: 56010.01 $zp.copy [1] 3.078884 $p.e [1] 0.715543 $shape.e [1] 0.1971554 $scale.e [1] 1.328558 $u.v [1] 57.375 $var.v [1] 880.9596 I am not sure if the "warning" produced above affects the results? Also, I am not quite sure what are the meanings of "iter" values above as I could not find the meaning of these terms from the literature. Thanks for anyone that could help.

07-17-2011, 10:21 PM	#2
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	Don't crosspost. Your other post was deleted. One post, one location.