I have often downloaded datasets from the SRA where the authors failed to mention which adapters were trimmed during the processing.
Local alignments tend to overcome this obstacle, but it feels a bit barbaric.
fastQC works occasionally to pick them up, but sometimes fails to find the actual adapter sequences.
Usually, I ended up looking up the kits they used and trying to grep for all the possible barcodes.
Is there a more robust/efficient way to do this?