Question: IGV custom Genome
0
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3.6 years ago by
####200
####200 wrote:

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 ?

igv software error • 1.3k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by ####200

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

ADD REPLYlink written 3.6 years ago by WouterDeCoster44k

maybe you need to zoom more?

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Medhat8.7k

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!

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by ####200
1

@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.

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by genomax85k
1
gravatar for ####
3.6 years ago by
####200
####200 wrote:

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.

ADD COMMENTlink written 3.6 years ago by ####200
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