SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
less PhiX than you think? beardy_man Illumina/Solexa 1 11-08-2013 12:50 PM
PhiX contamination MoritzF Illumina/Solexa 3 08-06-2013 05:49 PM
PhiX index HMorrison Illumina/Solexa 6 09-28-2011 07:09 AM
V3 PhiX kthai Illumina/Solexa 0 04-01-2011 12:21 PM
PhiX Spiking DavidBaker Illumina/Solexa 0 09-24-2010 08:35 AM

Reply
 
Thread Tools
Old 07-30-2014, 05:00 AM   #1
jamimo
Junior Member
 
Location: Kenya

Join Date: Oct 2013
Posts: 1
Default PhiX removal

Hi all,
I am trying to removed Phix reads from my miseq data but I keep on getting
# reads processed: 839305
# reads with at least one reported alignment: 0 (0.00%)
# reads that failed to align: 839305 (100.00%)
No alignments
The bowtie command used is - bowtie PhiX_index --sam --al aligned.fq --un unaligned.fq -1 ~/misedata/phixinput/13_S13_L001_R1_001.fastq.out -2 ~/misedata/phixinput/13_S13_L001_R2_001.fastq.out S13.sam

could someone tell me where the problem is?
Thanks,
Joshua
jamimo is offline   Reply With Quote
Old 07-30-2014, 05:17 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800
Default

Your sequencing facility may have already removed the phiX sequences when they processed your data. The result you are looking at may be real i.e. there is no phiX sequence in your sample file. You should ask the facility if they have removed phiX sequences.

Last edited by GenoMax; 07-30-2014 at 05:41 AM.
GenoMax is offline   Reply With Quote
Old 07-30-2014, 09:53 AM   #3
westerman
Rick Westerman
 
Location: Purdue University, Indiana, USA

Join Date: Jun 2008
Posts: 1,104
Default

I agree with GenoMax - you probably do not have any phiX reads. If you want to test this out you could put part of phiX at the end of your read files (making copies of them first!) and see if you get one hit. In other words deliberately contaminate your reads.
westerman is offline   Reply With Quote
Old 04-06-2015, 04:58 AM   #4
maivantan
Member
 
Location: Vietnam

Join Date: Oct 2013
Posts: 51
Default

Can anyone please help me which web i can downloan PhiX genome fastq file?
Thank you very much.
maivantan is offline   Reply With Quote
Old 04-06-2015, 05:13 AM   #5
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,800
Default

From iGenomes (if you want Illumina's version, it is there): http://support.illumina.com/sequenci...e/igenome.html This is a package download with indexes etc but you will find the genome fasta file there. If you need it in fastq format then you could made a fake set of Q-scores.
GenoMax is offline   Reply With Quote
Old 04-06-2015, 05:50 AM   #6
maivantan
Member
 
Location: Vietnam

Join Date: Oct 2013
Posts: 51
Default

Thank you very much GenoMax
maivantan 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 06:01 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO