Hello!
Thank you so much for your great work.
I am relatively new to working with biological data. I need FPKM normalized data, and from what I understand the transcription data available so far corresponds to the ?glass_expression.txt.gz? file that contains RPKM made for paired-end RNA-seq (Wang, 2017), and the ?glass_transcript_counts.txt.gz? file that contains the expected length and counts obtained from Kallisto (not yet normalized to TPM), and not including the effective length.
Is there any way we can get access to the counts from which you obtained the normalized RPKM data (PRADA pipeline)? I need them for FPKM normalization.
Thank you in advance.
Jessica Valdebenito
Created by Jessica Valdebenito jvals Hi Jessica,
Unfortunately we no longer have the counts from the PRADA pipeline. The postdoc who was involved in that study is no longer in the lab, and the RPKM data that is on Synapse is directly from Wang, 2017 publication you reference. We hope to have more comprehensive expression data for the cohort at a later date, but it is still under development right now. I'm sorry I can't be of more help at this time.
Fred