bwa fail to infer insert size

Question

[0range]

Hello! I am using bwa aln for paired-end small RNA-seq reads. After trimming adapters and QC, the reads are 15-150bp For most of my samples all looks well after sampe, but for a few of them I get the message:

[infer_isize] fail to infer insert size: upper bound is smaller than read length

It still outputs a SAM file, but there are no mapped reads. I'm unsure what is causing the message? Any insight is appreciated!

Answer 1

[GenoMax]

For small RNA you should use something like bowtie v.1 instead.

[0range]

Ok, thanks for the suggestion. But any ideas as to what the message I'm getting means?

[ATpoint]

The insert size is shorter than the read length means the reads overlap.