Visualize contigs from de novo assembly

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Lu Zhang

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Nov 10, 2016, 6:35:59 PM11/10/16
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Hi,

We are trying to visualize the contigs generated from de novo assembly on IGV. But the graph seems weird.
The steps are as:
1. Contigs are assembled by Supernova with fasta format.
2. Align these contigs to the reference genome by Bwa mem.
3. import the bam file to IGV.

I have uploaded the screenshot for both bam file (bam.png) and IGV (igv.png). Does anybody have experience on this issue?

Thank you

Eric
bam.png
igv.png

Lu Zhang

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Nov 13, 2016, 12:45:05 PM11/13/16
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Anybody has ideas about that?

Lu Zhang於 2016年11月10日星期四 UTC-8下午3時35分59秒寫道:

James Robinson

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Nov 13, 2016, 4:08:46 PM11/13/16
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Could you frame your question more precisely?  If it's a question about IGV you are just seeing what is present in your file.   If it's a question about your experiment this is probably not the right forumn.

Jim


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