If you are using easyRNASeq and if you see the following error
This is because the chromosome name from annotation file is different to the headers of bam files.
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
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.
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PHDcell: the best online free reference manager
Code:
Error in .doBasicCount(obj) : The genomicAnnotation slot is empty
Code:
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"
Code:
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"
It is usually not possible to change biomaRt chromosome names. But you can update the bam headers by
Code:
samtools reheader header.sam in.bam > out.bam
Ok, now it is all set. It took me one whole day to figure out, cheers.
==============================================
PHDcell: the best online free reference manager