Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
problems understanding pileup format pi101 Bioinformatics 2 11-14-2012 03:47 PM
Who's running Quake? chrishah Bioinformatics 8 02-23-2012 12:55 AM
Problems with running Quake vivienne_lovely Bioinformatics 1 01-18-2012 09:32 AM
which one indicate strand on bowtie outputs? tujchl Epigenetics 3 03-23-2011 06:20 PM

Thread Tools
Old 07-17-2011, 10:09 PM   #1
Junior Member
Location: Australia

Join Date: Jul 2011
Posts: 1
Default 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
value: 56010.01
[1] 3.078884

[1] 0.715543

[1] 0.1971554

[1] 1.328558

[1] 57.375

[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.
zlix425 is offline   Reply With Quote
Old 07-17-2011, 10:21 PM   #2
--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.
ECO is offline   Reply With Quote

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off

All times are GMT -8. The time now is 05:40 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO