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fastqc result: whether trim off low quality reads or not

Hi friends and colleagues

I have run 78 wgs metagenomic sequences (submitted sequences from other studies in SRA) with fastqc followed their result accumulation by multiqc. I have got some result like this attachment. I am confused whether to trim bases with phred qualty score 20. Because, in that case a lot of sequence will become much shorter. And in that case, it will negatively affect the maping with bowtie aligner. Is my understanding true? What should I do in this case?

next-gen fastqc multiqc
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updated by Pierre Lindenbaum Pierre Lindenbaum • written by dpc dpc

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written by Ram Ram

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