How to do a PCA plot on the exome data using different library kits?

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4.7 years ago

mullin.yu • 0

Hi,

I have around 1000 exome data (fastq, bam, vcf). I want to a PCA plot on the exome data using different library kits for the QC step. I would expect the PCA plots showing clusters of samples using different library kits.

May I know any suggestion? Any software package can help? Use BAM or VCF file?

Thanks a lot!

Regards, Mullin

Exome PCA Library-kit exome sequencing • 1.0k views

ADD COMMENT • link updated 5 months ago by ATpoint 85k • written 4.7 years ago by mullin.yu • 0

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Produce PCA bi-plot for 1000 Genomes Phase III - Version 2

This should give you an idea.

ADD REPLY • link 4.7 years ago by ATpoint 85k

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Hi, there. Have you got any ideas?

ADD REPLY • link 5 months ago by David-walson • 0

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Ideas for what? Please open a new question if you need help.

ADD REPLY • link 5 months ago by ATpoint 85k

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