Question: How to load BAM files that do not have chromosome name in the header?
gravatar for JC
4 weeks ago by
JC0 wrote:

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.

igv rna-seq • 102 views
ADD COMMENTlink modified 4 weeks ago by WouterDeCoster35k • written 4 weeks ago by JC0

I added (code) markup to your post for increased readability. You can do this by selecting the text and clicking the 101010 button. When you compose or edit a post that button is in your toolbar, see image below:

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ADD REPLYlink written 4 weeks ago by WouterDeCoster35k
gravatar for Chris Miller
4 weeks ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

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 written 4 weeks ago by Chris Miller20k
gravatar for swbarnes2
4 weeks ago by
United States
swbarnes24.5k wrote:

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 written 4 weeks ago by swbarnes24.5k

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

ADD REPLYlink written 4 weeks ago by JC0
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