search

gersteinlab / texp

TeXP is a pipeline to gauge the autonomous transcription level of L1 subfamilies using short read RNA-seq data
Apache License 2.0
5 stars 1 forks source link

Effective L1HS transcript lengths #6

Closed yanwu2014 closed 2 years ago

yanwu2014 commented 2 years ago

Hi! I was wondering how I could extract the L1Hs transcript lengths you guys used to compute RPKM from counts?

Thanks! Yan

fabiocpn commented 2 years ago

Thank you for your interest, Yan. L1Hs transcripts should have ~6000 bases. Our estimates were derived from long-read RNA-seq. If I remember correctly, we used PacBio to estimate the average transcript length. There is no reason to believe that transcript length will dramatically differ between L1Hs, L1PA2, and L1PA3.

Feel free to reach out if you have additional questions.