Quality control of genomic resequencing data from a HiSeq

[gavin.oliver]

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.

[chongm]

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.

[vishnuamaram]

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.