sRNA-seq. Adapter-primer contamination

Question

[joaquinj12]

Hi,

I have Illumina smallRNA-seq samples with an amount of adapters (whole sequence, maybe adapter-primer contamination) around 70% of total raw reads in the fastq file. I am removing the adapters with cutadapt from the 3', so finally the number of total reads decreases substantially. I would like to know if the adapter-primer contamination may bias the biological differences in my samples. Are the real sRNA transcripts being sequenced, or are they hidden by the adapters?

Thanks,

Joaquín