Entering edit mode
6.9 years ago
Pin.Bioinf
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340
Hello, I built a summarized experiment with summarized overlaps by using the UCSC gtf annotation file and I got the object se.
library(TxDb.Hsapiens.UCSC.hg38.knownGene)
ebg <- exonsBy(TxDb.Hsapiens.UCSC.hg38.knownGene, by="gene")
se <- summarizeOverlaps(features=ebg, reads=bamfiles,
mode="Union",
singleEnd=TRUE,
ignore.strand=FALSE,
fragments=FALSE )
But when I print it, I get this:
> assay(se)
[,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12] [,13]
1 425 293 1273 1531 878 142 153 597 266 3929 1499 1655 751
10 73 50 127 118 115 82 65 194 73 311 153 671 561
100 5 1 5 15 10 16 17 41 42 27 14 4 12
1000 134 95 105 139 95 176 110 243 140 219 96 130 81
10000 26 23 1 4 2 12 9 32 25 16 12 17 12
100008587 0 0 0 0 0 0 0 0 0 0 0 0 0
100008589 0 0 0 0 0 0 0 0 0 0 0 0 0
100009613 0 0 0 0 0 0 0 0 0 0 0 0 0
100009676 8 10 11 14 8 26 30 89 55 22 20 23 4
10001 49 41 31 52 24 79 73 154 136 74 104 171 175
10002 1 0 0 0 0 0 0 1 0 0 1 0 0
10003 0 0 1 0 0 0 0 0 0 0 0 0 0
100033413 0 0 0 0 0 0 0 0 0 0 0 0 0
100033414 3 4 3 3 0 2 2 2 1 0 0 0 3
100033415 0 0 0 0 0 0 0 0 0 0 0 0 0
100033416 0 0 0 0 0 0 0 0 0 0 0 0 0
100033417 0 0 0 0 0 0 0 0 0 0 0 0 0
100033420 1 0 1 0 1 0 0 0 0 0 0 0 0
Did I do something wrong? What are those IDs? (100033413,10002,10001,... ) What happened to my UCSC IDs? or what database do they belong to? How could I annotate these genes when I finish the DE analysis?
Thank you very much.