I cannot view a BAM file with IGV
It complains that "File RNAseq_no1.bam does not contain any sequence names which match the current genome. File: hg19_refGene_NM_032291, hg19_refGene_NM_032785, hg19_refGene_NM_018090, hg19_refGene_NM_052998, ... Genome: chr1, chr2, chr3, chr4, ..."
I have take look at the head file with samtools:
samtools view -H RNAseq_no1.bam
Here are the first couple lines in the Header:
@HD VN:1.0 GO:none SO:queryname
@SQ SN:hg19_refGene_NM_032291 LN:4894
@SQ SN:hg19_refGene_NM_032785 LN:3188
@SQ SN:hg19_refGene_NM_018090 LN:2281
@SQ SN:hg19_refGene_NM_052998 LN:2382
@SQ SN:hg19_refGene_NM_001145278 LN:2203
It doesn't contain any chromosome name. I think this is what IGV complains about.
Does anyone know how I can possibly load the BAM files into IGV?