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Question: How to load BAM files that do not have chromosome name in the header?
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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?

Thank you.

ADD COMMENTlink 15 months ago JC • 0 • updated 15 months ago WouterDeCoster 39k
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ADD REPLYlink 15 months ago
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It looks like you have a sequence data that was aligned to a transcriptome, rather than a genome. If you want to use IGV, you will either need to a) create a new "genome" for IGV with one contig per gene (this is almost certainly not what you want) or b) align your RNAseq data to a genome, using something like HISAT2, STAR, etc.

ADD COMMENTlink 15 months ago Chris Miller 20k
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Those bam files were made by aligning to a list of transcripts. You cannot view them in IGV as aligned to chromsomes, but you can load the fasta of transcripts into IGV, and look at them by transcript.

ADD COMMENTlink 15 months ago swbarnes2 5.7k
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Could you tell me step-by-step how to do it?

ADD REPLYlink 15 months ago
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