Hi,
I recently downloaded a GEO dataset of paired end reads using SRAtool kit with the fastq-dump command. I performed quality check on these reads using FastQC, there were no overrepresented sequences nor detected adapter content in the raw data. I also manually inspected the bases at the ends of the reads from the Fastq file and no obvious repetitive sequences were observed.
However, the FastQC report indicates that all reads have a consistent length of 100 base pair. This seems quite odd, because after adapter removal, I would expect a range of sequence lengths between the minimum and the maximum. Author mentioned in article that raw reads were trimmed with FASTQ Trimmer (version 1.0.0).
Does FASTQ Trimmer perform absolute sequence length trimming (instead of trimming on known adapter sequences)? Also, were reads already trimmed prior uploading to GEO?
