Potential QC metrix
35bp... Post trim
Mean insert size 200bp
Mean tin ~70
Mapped reads ~15M
Current ENCODE Standards:
Experimental guidelines for bulk RNA-seq experiments can be found here.
- A bulk RNA-seq experiment is an RNA-seq assay in which the average library insert size is 200 base pairs. Experiments should have two or more replicates. Assays performed using EN-TEx samples may be exempted due to limited availability of experimental material.
- Each replicate should have 30 million aligned reads, although older projects aimed for 20 million reads.
Best practices for ENCODE2 RNA-seq experiments have been outlined here.
- Replicate concordance: the gene level quantification should have a Spearman correlation of >0.9 between isogenic replicates and >0.8 between anisogenic replicates (i.e. replicates from different donors).
- The experiment must pass routine metadata audits in order to be released.