IGV custom Genome

Question

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I have aligned reads with few genes and to view the alignment (bam) file I have loaded those gene sequence to IGV as a custom gene , but unfortunately I could see the alignment with only one gene(note: this gene is smallest in length amongst all) .

I have checked the SAM file to see if the reads has actually aligned properly to these gene or not , the alignment has worked fine and reads were aligned to all the genes, but somehow I am unable to view it in IGV.

I have no idea what could be the reason, any inputs on this ?

[WouterDeCoster]

What does it mean "I am unable to view it in IGV"? How does it look like? Have you tried zooming?

[Medhat]

maybe you need to zoom more?

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We believe that this post is solved.

For this reason I am closing your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[GenoMax]

@minz: Please don't delete/close posts that have a solution (I have restored the question). This solution is useful for others down the road if they run into same/similar issue.

You can accept your own answer as "correct" (click check mark against the answer) and provide closure to the original question.

Answer 1

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I figured out what was the problem. The problem was with the sequence header , the header( the sequence identifier) should be same in both the files bam file and genome file loaded in the IGV.