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 below. 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?
Thanks and regards, DC7