SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Building bowtie index with mirBase hairpin.fa file Gators RNA Sequencing 6 05-07-2015 11:43 AM
bowtie index problem (bowtie-build and then bowtie-inspect) tgenahmet Bioinformatics 4 09-10-2013 11:51 AM
PhiX index HMorrison Illumina/Solexa 6 09-28-2011 06:09 AM
bowtie index file jay2008 Bioinformatics 1 09-15-2011 01:42 AM
Bowtie-build index file generation, no *.3.ebwt, *.4.ebwt Bardj Bioinformatics 4 12-18-2009 09:32 AM

Reply
 
Thread Tools
Old 01-17-2012, 08:55 AM   #1
wingtec
Member
 
Location: Charlottesville, VA

Join Date: Apr 2010
Posts: 34
Default index file of phiX to use in Bowtie

Hi All,

I wonder if someone can direct me to find a copy of the index file for phiX to be used in Bowtie. I am pretty sure someone has made it available somewhere.

Best,

Yongde
wingtec is offline   Reply With Quote
Old 01-17-2012, 09:01 AM   #2
kopi-o
Senior Member
 
Location: Stockholm, Sweden

Join Date: Feb 2008
Posts: 319
Default

Why not download the phiX genome sequence and run bowtie-build on it? It won't take a minute.
kopi-o is offline   Reply With Quote
Old 01-17-2012, 11:22 AM   #3
wingtec
Member
 
Location: Charlottesville, VA

Join Date: Apr 2010
Posts: 34
Default

Thanks. You are absolutely right. It is much easier building your own than looking for one.

Yongde
wingtec is offline   Reply With Quote
Old 01-18-2012, 02:51 AM   #4
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

Join Date: May 2011
Posts: 838
Default

I've had matches to regions spanning the start/end sequence (i.e. to a circular phiX genome) on an Illumina run, so it might be worth tacking a few bases from the start of the sequence onto the end of your sequence.
gringer is offline   Reply With Quote
Reply

Tags
bioinfomatics

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 02:57 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO