rsem-calculate-expression -p 12 --star --append-names --star-path /usr/local/bin/ --star-gzipped-read-file /data/sample1.fastq.gz /genome/GRCh38_RSEM_STAR sample > sample_RSEM.log 2>&1
Started job on | Jun 16 04:09:46
Started mapping on | Jun 16 04:10:58
Finished on | Jun 16 04:13:01
Mapping speed, Million of reads per hour | 488.85
Number of input reads | 16702488
Average input read length | 49
UNIQUE READS:
Uniquely mapped reads number | 11145815
Uniquely mapped reads % | 66.73%
Average mapped length | 49.18
Number of splices: Total | 501431
Number of splices: Annotated (sjdb) | 490452
Number of splices: GT/AG | 496455
Number of splices: GC/AG | 4424
Number of splices: AT/AC | 328
Number of splices: Non-canonical | 224
Mismatch rate per base, % | 0.28%
Deletion rate per base | 0.01%
Deletion average length | 1.67
Insertion rate per base | 0.01%
Insertion average length | 1.35
MULTI-MAPPING READS:
Number of reads mapped to multiple loci | 4302351
% of reads mapped to multiple loci | 25.76%
Number of reads mapped to too many loci | 59784
% of reads mapped to too many loci | 0.36%
UNMAPPED READS:
Number of reads unmapped: too many mismatches | 20167
% of reads unmapped: too many mismatches | 0.12%
Number of reads unmapped: too short | 1055479
% of reads unmapped: too short | 6.32%
Number of reads unmapped: other | 118892
% of reads unmapped: other | 0.71%
CHIMERIC READS:
Number of chimeric reads | 0
% of chimeric reads | 0.00%
1254322 7219415 0 8473737
4632069 2587346 4804035
24264981 1
0 1254322
1 2415380
2 1356563
3 1468225
4 444324
5 448121
6 200991
7 138113
8 413042
9 47136
10 112856
11 17339
12 20372
13 11737
14 16524
15 9874
16 6305
17 13935
18 10011
19 5951
20 5897
21 5531
22 2173
23 3960
24 2891
25 1498
26 5893
27 1658
28 2301
29 577
30 1346
31 3768
32 1992
33 1365
34 359
35 1205
36 4698
37 730
38 195
39 165
40 1693
41 330
42 598
43 67
44 212
45 1203
46 5
47 31
48 1009
49 949
50 354
52 34
53 39
54 245
55 20
56 3824
57 1
58 9
59 14
60 182
62 68
63 86
64 35
65 9
66 169
68 17
70 1246
71 20
72 371
73 144
74 10
76 27
78 31
80 1352
81 8
84 2
Inf 0
--
RSEM website: http://deweylab.biostat.wisc.edu/rsem/
---
You received this message because you are subscribed to the Google Groups "RSEM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to rsem-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/rsem-users/5522511b-2578-448b-a8ce-17590b189d6ao%40googlegroups.com.
Dear Bo,Thanks for the fast response. I have two additional questions:
1. I used rsem-prepare-reference, supplied GTF file and prepared STAR indices for human transcriptome. So, could you please explain what you mean by saying "STAR aligns to the genome"? Aren't these indices for transcriptome sequences?
2. Counting reads with SAM flag 0x4 gives the total unaligned reads (1254322), as also reported in .cnt file. The total unmapped reads reported by STAR is 1194538. Shouldn't these two be identical?
--
RSEM website: http://deweylab.biostat.wisc.edu/rsem/
---
You received this message because you are subscribed to the Google Groups "RSEM Users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to rsem-users+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/rsem-users/4628152c-a975-4959-ac3d-85d595287989o%40googlegroups.com.