trimming A tails: clip3pAdapterSeq in star vs cutadapt

Question

[wiscoyogi]

I'm working with a smRNA-seq dataset, where the smRNAs were polyadenylated and need to be removed before mapping to the genome.

The library prep manufacturer said to trim 15 As, but sometimes it's longer and cut adapt can adapt to this and trim past that (which is good). But then, I get some reads that are zero. So then when I use STAR for Alignment, STAR crashed!

So I was going to add the flag --minimum-length 0 to my cut adapt command to remediate this. but, why bother with cutadapt if star can handle it?

Question: I wanted to just use the --clip functions in STAR. however, there isn't much documentation on clip3pAdapterSeq beyond the short description in the manual -- if I tell it to trim 15 As, and I have a sample with say 20 polyA tails, and I do --clip3pAdapterSeq AAAAAAAAAAAAAAA (e.g. 15 A) , will STAR trim that to AAAAA (5 As left) or will it completely eradicate the read?

thank you!

[GenoMax]

With small RNA you may just want to use bowtie v.1 instead of STAR. Clip the poly-A's using cutadapt or bbduk.sh.