Hi,
Is it possible to have count version of the validation RNAseq data sets. Both the validation RNAseq have only TPM version.
Thanks.
Created by Ramyar Molania Ramyar Dear Mark,
It would be really great if you could provide RNAseq counts with Ensembl gene ids for RNAseq validation data sets.
Thanks,
Ram.
Dear Mike,
I usually use the better normalization approaches to normalize RNAseq data which they need raw counts.
I will add more post about that after.
Thanks,
Ram.
Not necessarily. The community phase is usually where top performing teams are invited to help prepare a manuscript. If there is possible insight from using RNA-seq counts, challenge organizer might be interested in a bonus question. Alternatively the use of counts could be explored in the community phase as you point out. i thought that is just called 'the community phase' Dear Ram,
Once the challenge ends we may consider adding a bonus challenge. If you like you could explain your reason for wanting the counts (after the validation round ends) and it might motivate a bonus challenge. Dear Ram,
Unfortunately we are not providing count data for the validation datasets. I understand that there are a lot of things one could do with the counts like determine total reads per sample but we decided early on to only provide TPMs. The MMRF data is public so we provided everything for it. Hi again,
It would be great to have the all the versions of RNAseq (you provided as training sets) in validation cohort.
Thanks.