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Old 05-03-2011, 03:40 AM   #1
gavin.oliver
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Location: uk

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Default Quality control of genomic resequencing data from a HiSeq

Hi all,

We will soon be outsourcing some targeted genomic resequencing on the HiSeq.

I am just wondering, beyond the onboard qulaity value generation and filtration performed by the service provider, what other quality checks should be perfrom subsequently ourselves?

Any input would be appreciated.
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Old 03-05-2013, 07:59 AM   #2
chongm
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I would suggest using a program known as FASTQC, which gives you a lot of summary metrics for read quality, GC content, duplication levels, overrepresented sequences. It's fast and provides very nice graphs for troubleshooting.
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Old 06-30-2013, 01:48 AM   #3
vishnuamaram
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Hi chongm,

I have genome seq.data of human lymphocytes done on illumina hiseq2000 paired end 2X100bp,
I had done FASTQC and trimmed low quality bases by FASTX tool kit.

I am really struck to go further, kindly explain in detail clarity about indexing human reference genome hg19.

Thank you,
Vishnu.
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