Getting raw read counts directly

[chbk]

Would it be possible to get raw read counts directly from Stringtie, instead of coverage values to transform with prepDE.py?

I understand prepDE.py uses a formula that gives an estimate of the original raw counts, but it requires a fixed read length, which is not practical in our case. We have concatenated files made from experiments with different read lengths, so there is no single read length we can use for the formula.

The read counts are needed for differential analysis, so getting that without applying a formula to get an estimate of the original value would be the best way to go.

[dadrasarmin]

Hi @chbk,

Have you found a solution to this problem? I have a similar problem.

[chbk]

No I haven't found a straightforward way. Our RNA-Seq pipeline (https://github.com/FAANG/analysis-TAGADA) checks that read lengths are approximately equal before running prepDE.py.