Bulk RNA-seq, pasilla Drosophila knockdown vs control, Wave 2 (2026-05-06)
phalaena:run:PA-R-3-1-wave2-2026-05-06
Wave 2 bulk RNA-seq run of paper 3.1 (Brooks 2011 pasilla knockdown vs control, Drosophila melanogaster S2-DRSC cells). Four samples in a mixed library layout: two single-end untreated controls (SRR031708, SRR031709) and two paired-end knockdowns (SRR031714, SRR031716), quantified with Salmon against the BDGP6 transcriptome. The run completed end-to-end in 27 minutes (validation snapshot). It is marked SUCCESS (degraded): Salmon mapping landed in the 0.14-0.24 percent band because the 2010-vintage reads are 45 bp and Salmon's default k=31 index leaves only about 15 bp of effective seeding (validation finding #16). The degradation is a parameter-tuning artifact of the legacy read length, not a pipeline defect; the run reached SUMMARY and emitted a schema-conformant summary.json. This run also exercised mixed PE plus SE coexistence in one submission, after the SE-branch fix (finding #2).
- kind
- run
- pipeline
- Bulk RNA-seq pipeline, release p1.1
- status
- draft
- phalaena:run:PA-R-3-1-wave2-2026-05-06
View Bulk RNA-seq, pasilla Drosophila knockdown vs control, Wave 2 (2026-05-06) on the Phalaena Wiki