Aligner | GRCh38-local | GRCh38 | T2T | |
|---|---|---|---|---|
star_salmon |
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star_rsem |
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hisat2 |
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SALMON vs. RSEM gene counts:
No significant changes in feature count values observed for “gene_counts” produced by RSEM or SALMON (see figure below). Comparison based on 45,315 commonly reported genes by SALMON (n=51,912) and RSEM (n=45,706).
Most significant changes observed are similar across all samples, hence, differential expression analysis should produce similar results for SALMON and RSEM.
...
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%) |
Example - RSEM unique genes:
| Code Block |
|---|
gene_id transcript_id(s) SRR20622172 SRR20622173 SRR20622174 SRR20622175 SRR20622176 SRR20622177 SRR20622178 SRR20622179 SRR20622180
ENSMUSG00000003178 ENSMUST00000077159 978.00 889.00 712.00 716.00 911.00 819.00 1065.00 1214.00 1566.00
ENSMUSG00000029333 ENSMUST00000031276,ENSMUST00000166484,ENSMUST00000166632,ENSMUST00000168092 386.00 256.00 173.00 160.00 358.00 212.00 419.00 508.00 553.00
ENSMUSG00000032134 ENSMUST00000034653 12.00 20.00 374.00 445.00 16.00 539.00 29.00 64.00 98.00
ENSMUSG00000035349 ENSMUST00000021384 204.00 177.00 103.00 112.00 187.00 137.00 43.00 56.00 67.00
ENSMUSG00000038194 ENSMUST00000127256,ENSMUST00000137350,ENSMUST00000155591 7.00 16.89 15.22 10.81 15.00 11.24 44.72 32.92 40.82
ENSMUSG00000042402 ENSMUST00000045546 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000043858 ENSMUST00000057195,ENSMUST00000107891,ENSMUST00000136861 2727.91 1965.92 668.00 643.00 2571.96 750.93 786.96 1097.95 1152.00
ENSMUSG00000045946 ENSMUST00000056234 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000047490 ENSMUST00000050983 0.00 0.00 4.00 3.00 1.00 5.00 1.00 1.00 0.00
ENSMUSG00000048665 ENSMUST00000054470 0.00 0.00 0.00 1.00 0.00 0.00 0.00 0.00 1.00
ENSMUSG00000050347 ENSMUST00000052897 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000050431 ENSMUST00000051453 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000050604 ENSMUST00000062454 6.00 3.00 3.00 3.00 8.00 4.00 5.00 3.00 6.00
ENSMUSG00000050781 ENSMUST00000062407 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000051052 ENSMUST00000156004 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000052429 ENSMUST00000045325,ENSMUST00000085387,ENSMUST00000107840,ENSMUST00000107842,ENSMUST00000107843,ENSMUST00000125886,ENSMUST00000127531,ENSMUST00000153576 6824.00 4330.00 1250.00 1438.00 6072.00 1652.00 1675.00 2254.00 2492.00
ENSMUSG00000054758 ENSMUST00000067972 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000055099 ENSMUST00000068485 0.00 0.00 1.00 3.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000055694 ENSMUST00000046516 0.00 0.00 0.00 0.00 0.00 0.00 0.00 1.09 0.00
ENSMUSG00000056106 ENSMUST00000070021 4.00 1.00 8.90 3.00 3.00 1.00 5.00 6.00 4.00
ENSMUSG00000056606 ENSMUST00000070814 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000056872 ENSMUST00000077868 0.00 0.00 1.00 1.00 0.00 3.00 0.00 0.00 0.00
ENSMUSG00000057351 ENSMUST00000078761 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000057626 ENSMUST00000076465 2.49 0.00 2.49 2.50 8.69 2.49 3.44 8.99 7.58
ENSMUSG00000057832 ENSMUST00000080925 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000057924 ENSMUST00000072427 56.97 31.00 43.98 51.00 66.00 41.31 60.00 52.00 61.00
ENSMUSG00000059041 ENSMUST00000080251 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000059101 ENSMUST00000079234 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000059227 ENSMUST00000073059 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000059448 ENSMUST00000079465 0.00 0.00 2.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000059511 ENSMUST00000071632 0.00 0.00 2.36 0.00 2.63 0.00 1.91 2.51 0.00
ENSMUSG00000059731 ENSMUST00000071975 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000059996 ENSMUST00000073580 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000060393 ENSMUST00000122096 6.30 1.74 3.69 1.24 3.74 1.19 1.20 4.84 2.58
ENSMUSG00000060559 ENSMUST00000074466 3.00 0.00 16.00 11.00 0.00 14.00 14.00 30.00 30.00
ENSMUSG00000061075 ENSMUST00000077247 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000061305 ENSMUST00000074192 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000061501 ENSMUST00000080031 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
ENSMUSG00000061777 ENSMUST00000076936 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 |
Run time comparison
GRCm38-local star_salmon | GRCm38-local star_rsem | GRCm38 star_salmon | GRCm38 star_rsem | T2T star_salmon | T2T star rsem | |
|---|---|---|---|---|---|---|
Duration | 1h 15m 33s | 1h 46m 52s | 1h 27m 22s | 2h 57m 55s | 2h 2m 59s | 2h 35m 30s |
CPU hours | 60.1 | 139.1 | 54.4 | 119.3 | 139.8 | 163.1 |
Wall time | 01:27:56 | 02:58:24 | 02:03:28 | 02:36:06 | ||
Memory | 4,194,304 kb | 4,194,304 kb | 4,194,304 kb | 4,194,304 kb |