Read alignment anomaly

Question

[daewowo]

I have aligned metagenomic reads to a genome, and find that at the 5' ends of the reads often there is no alignment to the genome - this is indicated by the multicoloured regions in the plot blow. Solid blue and solid pink are perfectly aligned sections of reads (fwd and rev).

Any ideas why parts of reads would not align in such a consistent manner?

[Gregor Rot]

Are these soft-trimmed by the aligner? Did you do a quick quality check? (fastqc). Metagenomic sample and one reference genome alignment? Could also be some sample preparation bias? Just ideas

[daewowo]

Could be that adapters not clipped, need to check workflow

[daewowo]

Same result after trimming with fastp. These are metagenomic sample and one ref genome. fastqc didnt turn up any obvious anomalies to me. Suspect there is some odd sample prep. issue