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No significant changes in feature count values observed for “gene_counts” produced by RSEM or SALMON (see figure below)
Most significant changes observed are similar across all samples, hence, differential expression analysis should produce similar results for SALMON and RSEM.
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Table: Stats of uniquely reported gene counts by a SALMON or RSEM.
Tool | Unique genes | No expression (Zero counts) | Difference above (average count >=50) | Difference above (average count >=100) | Difference above (average count >=500) |
|---|---|---|---|---|---|
SALMON | 6,597 | 3,277 (49.7%) | 140 (2.1%) | 82 (1.2%) | 30 (0.4%) |
RSEM | 391 | 216 (55.2%) | 29 (7.4%) | 23 (5.9%) | 9 (2.3%) |