Question: Visualizing mpileup data
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rquigl01 • 10 wrote:
So far in my analysis of my NGS data, I have ran my files through bowtie2 which created a SAM file. I then converted that SAM file into a BAM file. My ultimate goal is to have all of the SNPs, SNVs, and INDELS in a table like manner for me to look at. I'm not really sure how to achieve this after creating the BAM file. I've tried mpileup, but when I open the vcf file in IGV and start to zoom in on a chromosome position, the program freezes. I also see no way of converting that SNP data into a easy to read data format. On galaxy it says that my mpileup data has over 100 million lines. I really only want to see the SNPs and INDELS. As you can probably tell, I'm a beginner to all of this. Any help would be greatly appreciated!
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modified 2.4 years ago
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Jennifer Hillman Jackson ♦ 25k
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2.4 years ago by
rquigl01 • 10
