a) Will RNA-seq be available for all training and validation samples? b) Will RNA-seq BAMs be available or just quantified gene expression? Thanks, David.

Created by David Knowles davidaknowles
Yes there will be salmon counts and TPMs for both gene level and transcript level. Please note the Challenge question two also has microarray cohorts for both the training and validation. If you are interested in splicing for prediction, Challenge question 3 may be best.
That's a shame but I understand the limitations with dbGAP. My interest was to quantify splicing variation - I guess this will be somewhat possible still since you say there will be transcript level rather than just gene level expression quantification? Thanks.
Hi David, Unfortunately neither RNA-seq fastq or bams will be available. We did consider how to do this for this challenge but it not viable. The MMRF sequencing data is hosted by dbGaP and we cannot provide pass-through access to it. Each individual would have to get dbGaP approval for access. That process can take 3 or more months so we are only providing post processed results.

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