Hi All, I have a general question about small RNAseq read size after trimming. I was able to trim my samples (sequenced with 50 bases long reads) with most of the reads resulting in 18-30 bases in length (which is expected of small RNA seq) after trimming. However, there are some reads that are still 50 bases long and their 3' region do not match with adapter sequence. Could it be possible for those reads to be pre-trimmed or come without 3' adapter justifying their length of 50 bases even after trimming? I was curious whether some of the reads could get sequenced without 3' adapter sequences. I would appreciate your expertise and clarification on this.
Could it be possible for those reads to be pre-trimmed or come without 3' adapter justifying their length of 50 bases
It is highly unlikely to have some reads trimmed and some untrimmed in the same file (unless someone merged different files), so I don't think they were pre-trimmed. On the other hand, it is indeed possible some longer reads passed the size selection step during library preparation.
Do you have a reference genome available? If yes, map those "longer" reads to the reference genome and check if they match it over the entire sequence. Then you will be at peace about their origin and quality.