So after using bbduk (adapter removal, quality trimming, and contamination filtering) I am going to use bbmap on the unmatched fastq1 and unmatched fastq2. I am assuming the matched file are those reads that were identical to the phix_adapters and therefore I do not want? Is this correct? Sorry, I am new to Illumina data. Also, should I use
to re-index before using bbmap?
Thank you .
Code:
bbmap.sh ref=hg19.fa
Thank you .
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