some problems of easyRNASeqâ : about the gtf files

Hu Fuyan [guest] guest at
Tue Mar 19 05:27:52 CET 2013

I want to use easyRNASeq to get exon counts. But I found a strange thing:

I have two human annotation files from different sources: one(Homo_sapiens.GRCh37.70.gtf.gz
 ) is from ensemble ftp (; the other(genes.gtf   ensembl) is from Illumina igenomes  (

The two annotation files are almost the same only with a small differentiation, such as the order of exons and attribute. 
When I run easyRNASeq, I used the two gtf files to check the result.

I have got different results for SLC25A13 exons

 -- output of sessionInfo(): 

Firstly,I got my bam file from tophat.

When I used Homo_sapiens.GRCh37.70.gtf as my annotation file in easyRNASeq, I got the result:

"\"ENSG00000004864\"_1" 2

"\"ENSG00000004864\"_2" 4

"\"ENSG00000004864\"_3" 16

"\"ENSG00000004864\"_4" 3

"\"ENSG00000004864\"_5" 7

"\"ENSG00000004864\"_6" 8

"\"ENSG00000004864\"_7" 5

"\"ENSG00000004864\"_8" 4

"\"ENSG00000004864\"_9" 4

"\"ENSG00000004864\"_10" 1

"\"ENSG00000004864\"_11" 6

"\"ENSG00000004864\"_12" 4

"\"ENSG00000004864\"_13" 4

"\"ENSG00000004864\"_14" 6

"\"ENSG00000004864\"_15" 8

"\"ENSG00000004864\"_16" 5

"\"ENSG00000004864\"_17" 3

"\"ENSG00000004864\"_18" 25

But when I used the gtf file from iIllumina igenomes, I got a wrong result (since we can view the bam form IGV):

"\"ENSG00000004864\"_18" 25

"\"ENSG00000004864\"_17" 13

"\"ENSG00000004864\"_2" 11

"\"ENSG00000004864\"_16" 3

"\"ENSG00000004864\"_1" 8

"\"ENSG00000004864\"_15" 5

"\"ENSG00000004864\"_14" 8

"\"ENSG00000004864\"_6" 6

"\"ENSG00000004864\"_13" 6

"\"ENSG00000004864\"_5" 0

"\"ENSG00000004864\"_3" 4

"\"ENSG00000004864\"_4" 4

"\"ENSG00000004864\"_12" 4

"\"ENSG00000004864\"_11" 4

"\"ENSG00000004864\"_10" 6

"\"ENSG00000004864\"_9" 1

"\"ENSG00000004864\"_8" 4

"\"ENSG00000004864\"_7" 4


I am so confused about the different result. 

Here are my main program using easyRNASeq:

count_gene_gtf_ensembl.table <- easyRNASeq(filesDirectory=getwd(),

When I changed the order of exons of gene SLC25A13 in genes.gtf (illumina) according to Homo_sapiens.GRCh37.70.gtf., I run easyRNASeq again. Then I got the right exon counts.  


Another problem is that I got the warning:" You enforce UCSC chromosome conventions, however the provided annotation is not compliant. Correcting it." When I used the gtf files from UCSC, I also got this warning.
How can I fix it? 

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