tRNAs in total RNA paired-end

[kbhit]

We were given a Long RNA dataset (paired-end) and are wondering if we can see tRNA expression in the bioinformatics data. Total RNA (no poly-a enrichment) was used in the library prep. Given that tRNA's may only be ~70nt in length - would you expect the paired-ended sequencing to pickup anything? I'm not sure if the small-ish size of the molecule will hinder any signal or not especially as it relates to how paired-end works.

Many thanks for your input

[Brian Bushnell]

Whether they are present may depend on what kind of size-selection was done during library prep. If you DO have 70bp molecules being sequenced, you should be able to find them with a paired-read overlapper like BBMerge.

bbmerge.sh in=read1.fq in2=read2.fq outm=merged.fq outu=unmerged.fq hist=hist.txt

"merged.fq" will now contain reads that successfully merged. So, you can look at the reads in that file that are around 70bp long (or whatever window you expect) and see if they are tRNAs.

Also, hist.txt will give you a histogram of observed insert sizes, which may be useful here.