For quantification: How long should the input sequences be?

[Lina Faller]

Hi all,

I have PE reads (2x76 bp) and trimmed my reads using Trimmomatic. After trimming, I found quite a few reads that were less than 10 bases in length.

My Trimmomatic arguments are somewhat stringent, so I'm not too surprised (LEADING:30, TRAILING:30, SLIDINGWINDOW:4:30).

For three recent samples, I calculated that about 12.5% of the forward reads were 10 bp or less and about 17% of the reverse reads.

My questions are:

1. Are these short reads even worth keeping around? 
   
2. Can Sailfish take advantage of them? 
   
3. Can I discard them? If yes, what is a good length to keep?
4. Are my Trimmomatic arguments too stringent?

Thanks for any advice!