How to determine phix read in undermined fastq files
1 answer
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
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.
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