Can we know if GTDB Sequences uses Poly(A) tails?

GTDB
1

Hello,
I want to map human scRNA-seq with poly(A) tails onto bacterial & viral genome. I want to know, if there are some bacterial sequences in GTDB that has poly(A) tails. Is there a way to filter this?

Thank you.

Best,
Fad

2

Hi Fad,

The genomes in GTDB come directly from the NCBI Assembly DB. These genomes are of varying quality and it is certainly possible some contigs in these genomes have poly(A) tails.

Cheers,
Donovan

3

Hi Donovan,

thank you for your feedback. Do you, or anyone in this forum, maybe know, if there’s a good program that can detect the poly(A)-tails in those sequences? I just don’t think it’s feasible to inspect the publication one by one, to see whether it has poly(A) tails…

Best,
Fad

4

Hi Fad,

You could take a look at fastp and in particular its polyX tail trimming feature:

Cheers,
Donovan