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

Question

[JC]

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.

[WouterDeCoster]

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Answer 1

[Chris Miller]

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.

Answer 2

[swbarnes2]

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.

[JC]

Could you tell me step-by-step how to do it?