How to determine phix read in undermined fastq files

Question

[1769mkc]

How to determine phix read from undermined fastq files ?

Answer 1

[GenoMax]

Align reads to the phiX genome provided by Illumina ( https://webdata.illumina.com/downloads/productfiles/igenomes/phix/PhiX_Illumina_RTA.tar.gz ) using any aligner or use bbduk.sh in filter mode to fish out reads for phiX.

$ bbduk.sh -Xmx10g in1=Undetermined_S0_L001_R1_001.fastq.gz in2=Undetermined_S0_L001_R2_001.fastq.gz ref=phiX.fa 

[1769mkc]

Thank you for the quick response, Can i segregate the phix reads from the other reads that was not assigned to the actual samples which woold be having index ?

[GenoMax]

Can i segregate the phix reads from the other reads

Do the following.

$ bbduk.sh -Xmx10g in1=Undetermined_S0_L001_R1_001.fastq.gz in2=Undetermined_S0_L001_R2_001.fastq.gz ref=phiX.fa k=21 outm=phix_discard.fastq.gz outu1=R1.fastq.gz outu2=R2.fastq.gz

phiX reads will be interleaved and collected in the phix_discard.fastq.gz file. Reads you want will be in other two files. If you don't want to collect phiX reads then simply omit outm=phix_discard.fastq.gz from command line.