reconstruct gene longer in 3 prime than associated isoforms

[jcleple33]

Hi! Running Cogent on isoseq3 data, after collapsing and filtering for 5' degraded isoform and reconstruction I have aligned the reconstructed gene and the different hq_isoforms. I do not understand how the Gene (0_0) sequence can have a longer 3prime end than the isoforms? Thanking you in advance for your help Sincerely, JC alignement3prime.txt

[Magdoll]

Hi @jcleple33 ,

It is difficult to tell what could result in the additional end sequence without seeing the whole input sequence set. Would you be wiling to share the input sequence privately? If you provide an email, I will request a secure upload of the input in.fa and the output cogent2.fa.

Thanks, --Liz

[Magdoll]

Closed unless further information given.

[jcleple33]

Closed unless further information given.

Hi! Sorry to be so late in my answer. Yes I send you my email : [email protected]

Thanks in advance JC