SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Quake!!!!!!!!!!!!!! iceice Bioinformatics 9 05-29-2012 11:41 PM
Quake install problem jjjscuedu Bioinformatics 0 04-19-2012 04:18 PM
Who's running Quake? chrishah Bioinformatics 8 02-22-2012 11:55 PM
Problems with running Quake vivienne_lovely Bioinformatics 1 01-18-2012 08:32 AM

Reply
 
Thread Tools
Old 12-28-2012, 08:21 AM   #1
Gators
Member
 
Location: North Carolina

Join Date: Feb 2011
Posts: 22
Default Quake

Anyone use Quake with Ion Torrent data. I know it won't correct the indels, but thought I would see how it behaved anyway.

I get this error:

Quote:
These reads must be longer than assumed. Increase the variable 'bitsize' in 'Read.h' to the read length.
Seems straightforward enough, except that I can't find the "Read.h" file anywhere. Nor is bitsize a documented option...
Gators is offline   Reply With Quote
Old 12-28-2012, 10:59 AM   #2
rflrob
Member
 
Location: Berkeley, CA

Join Date: May 2010
Posts: 50
Default

Read.h is a source code file (specifically, a header file). When I download quake, there's both a "bin" directory (containing BINary executables), and a "src" directory, which is where Read.h is. If you edit it in there, that should do the trick, then from the command line run "make; sudo make install" (or, if this is on a computer run by someone else, talk to them about appropriate ways to install it).

I'd also note that Quake claims to be "specifically intended for Illumina sequencing reads", so here's a gun, there's your foot, have fun!
rflrob is offline   Reply With Quote
Old 12-28-2012, 11:03 AM   #3
Gators
Member
 
Location: North Carolina

Join Date: Feb 2011
Posts: 22
Default

Ah yes, I saw that file shortly after I posted this...not sure where I was looking before when I claimed not to see it.

And for the record, yeah it doesn't really work...lost 30% of my reads, d'oh
Gators is offline   Reply With Quote
Reply

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 10:22 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO