Estimate the length of poly-A tails from randomly-primed RNAseq data So a poly-A tail is a long chain of adenine nucleotides that is added to a messenger RNA (mRNA) molecule during RNA processing to increase the stability of the molecule.

For my project, I would like to estimate the length of poly-A tails from randomly-primed RNAseq data. 

Any ideas how this could be done? Are there algorithms/tools which currently do this? 

Perhaps I would need to model this somehow? All suggestions appreciated
Can’t be done. If you already sequenced then I’m afraid the money is wasted (unless of course the data is good for something else).

The standard Illumina basecaller doesn’t deal well with homopolymers and will consequently call incorrect poly(A) lengths.

Amongst others, Narry Kim’s lab developed a dedicated method — TAIL-seq — to solve this problem. It’s a protocol for library prep using pulldown of biotin tagged tails (rather than random priming), plus dedicated basecalling software that uses spike-ins for calibration.

Be warned though: the protocol is reportedly technically challenging, and in order to use it you need an Illumina machine that gives you access to the raw image files before basecalling. Up-to-date Illumina machines won’t give you these files, full stop. So you’ll need to find a machine that runs an outdated firmware.