Solution for easyRNASeq Error in .doBasicCount(obj)

[weasteam]

If you are using easyRNASeq and if you see the following error

Error in .doBasicCount(obj) : The genomicAnnotation slot is empty

This is because the chromosome name from annotation file is different to the headers of bam files.

Chromosome infor from biomaRt:
 [1] "1"          "10"         "11"         "12"         "13"        
 [6] "14"         "15"         "16"         "17"         "18"        
[11] "19"         "2"          "3"          "4"          "5"         
[16] "6"          "7"          "8"          "9"          "GL456210.1"
[21] "GL456211.1" "GL456212.1" "GL456216.1" "GL456219.1" "GL456221.1"
[26] "GL456233.1" "GL456350.1" "GL456354.1" "GL456372.1" "GL456385.1"
[31] "JH584292.1" "JH584293.1" "JH584294.1" "JH584295.1" "JH584296.1"
[36] "JH584297.1" "JH584298.1" "JH584299.1" "JH584303.1" "JH584304.1"
[41] "MT"         "X"          "Y"

Chromosome infor from bam file:
 [1] "chr1"  "chr10" "chr11" "chr12" "chr13" "chr14" "chr15" "chr16" "chr17"
[10] "chr18" "chr19" "chr2"  "chr3"  "chr4"  "chr5"  "chr6"  "chr7"  "chr8" 
[19] "chr9"  "chrM"  "chrX"  "chrY"

The solution is to make sure the chromosome name is identical between your annotation file and the bam headers. eg. change 1 -> chr1.

It is usually not possible to change biomaRt chromosome names. But you can update the bam headers by

samtools reheader header.sam in.bam > out.bam

You can also change the chromosome name in reference before doing alignment.

Ok, now it is all set. It took me one whole day to figure out, cheers.


==============================================
PHDcell: the best online free reference manager