18 months ago by
I noticed that before, but not with RNAseq. It was a kind of artificial set up, where the sequence of interest was exactly 42 bases long, and so we sequenced for just 43 bases (so that there would be 42 bases with post-phasing data). And I noticed that a lot of reads had the last letter trimmed, but only if it was expected to be an A.
I remade the fastqs by turning off adapter trimming in the sample sheet, and that made all the reads 42 bases as they should be.
We were using a pretty old version of bcl2fastq for a while, so I can't vouch for the fact that newer versions will show this same behavior.