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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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sum of expected_count 1/100th of sum of uniquely mapped reads #80

Open patrickvdb opened 6 years ago

patrickvdb commented 6 years ago

If I sum the expected counts of an rsem run (from *.genes.results) I obtain about 59,000. However, If I understand correctly about 5.4M reads align uniquely (see .cnt file below). Where do my counts go?

cat ACAGTG-s_8.unassigned.cnt 
6331 5431432 0 5437763
5043361 388071 3030517
13042051 3
0       6331
1       2400915
2       1229311
3       744013
4       419705
5       269727
6       144174
7       84340
8       45229
9       32202
10      14378
11      13992
12      8405
13      5482
14      5558
15      2582
16      1477
17      1280
18      1199
19      1165
20      1256
21      1731
22      1357
23      314
24      326
25      923
26      209
27      67
28      31
29      26
30      2
31      2
32      2
34      4
37      16
38      1
39      28
40      1
41      2
Inf     0