bwa fail to infer insert size
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!
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