Bulk RNA-seq, polyA versus rRNA-depletion blood library-prep contrast, Wave 3 (2026-06-11)
phalaena:run:PA-R-3-4-wave3-2026-06-11
Wave 3 gap-fill run of paper 3.4 (Zhao 2018, the polyA+ versus rRNA-depletion clinical blood RNA-seq methods comparison). Four paired-end NextSeq 500 runs of human whole-blood RNA: two labeled as prepared by polyA+ selection (mRNA-seq, SRR6410613 and SRR6410614) and two as prepared by rRNA depletion (total RNA-seq, SRR6410617 and SRR6410618), quantified with Salmon against the pre-built GRCh38 plus GENCODE v46 transcriptome. SUCCESS at 04:48:10Z on 2026-06-10, 18.1 minutes wall clock (run id 683596ef). This is the first library-prep methods contrast in the bulk RNA-seq family. The two preparations mapped differently, but the other way round from the cited study: the libraries labeled polyA+ at about 31 percent and those labeled rRNA-depleted at about 85 percent (see QC and audit), for a run mean of 58.38 percent across 134,011 detected transcripts.
- kind
- run
- pipeline
- Bulk RNA-seq pipeline, release p1.1
- status
- reviewed
View Bulk RNA-seq, polyA versus rRNA-depletion blood library-prep contrast, Wave 3 (2026-06-11) on the Phalaena Wiki