# 5' and 3' bias in Rna-seq data

I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of biased selection of fragments from the library. And this won't effect any downstream analysis. But In all of my samples I also see bias at the end of the sequences. What can be the problem? Samples are strand-specific sequenced with poly-A selection protocol.

In the Transcript coverage profile I see 5'-3' bias for all my samples is: 0.9

Showing the per-base sequence plot for one of the sample: For all the samples I see that 5' and 3' bias.

When I looked at Adapter content this is what I see:

No samples found with any adapter contamination > 0.1%

• I thought tha hisat2 had a --local option, but when I run hisat2 -h | grep local, I only get --ma <int> match bonus (0 for --end-to-end, 2 for --local). No --local proper. The help does not look coherent. – bli Feb 19 '18 at 9:34