This is the sequence of illumina small RNA seq 3' adapter as reported everywhere:
if i trim this adapter only 0.2% of all the reads are trimmed.
Just by casual observation I noticed that the sequence "TGTAGGCACCA" is present in the 3' of 50% of the reads. It is not the case with another sample.
Is there a standard adapter sequence? If not then is there a tool for finding any unknown adapter? biopieces find_adaptor doesnt look for all kinds of possible adapters.