PhiX removal

[jamimo]

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

[GenoMax]

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.

[westerman]

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.

[maivantan]

Can anyone please help me which web i can downloan PhiX genome fastq file?
Thank you very much.

[GenoMax]

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.

[maivantan]

Thank you very much GenoMax