5' bias in Illumina captured sequecning

Mali Salmon · 04-13-2011, 12:46 AM

Hi All
We performed captured DNA sequencing of all exons belonging to 10 genes using MYselect kit (from MYcroarray company).
The sequencing was done using both Illumina and 454 platforms. When we plotted the average coverage across all captured regions (after dividing each exon to the same number of bins to account for the differences in exon length) we got very strong bias toward 5' of exons with Illumina, such that 5' of exons have higher coverage which decreases toward 3'. However, when we plotted a similar plot with 454 reads, we didn't see the bias, and got the bell shape curve.
Do you have any idea what could cause the bias in illumina sequences?
Thanks
Mali

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04-13-2011, 12:46 AM	#1
Mali Salmon Member Location: UK Join Date: Jul 2008 Posts: 24	5' bias in Illumina captured sequecning Hi All We performed captured DNA sequencing of all exons belonging to 10 genes using MYselect kit (from MYcroarray company). The sequencing was done using both Illumina and 454 platforms. When we plotted the average coverage across all captured regions (after dividing each exon to the same number of bins to account for the differences in exon length) we got very strong bias toward 5' of exons with Illumina, such that 5' of exons have higher coverage which decreases toward 3'. However, when we plotted a similar plot with 454 reads, we didn't see the bias, and got the bell shape curve. Do you have any idea what could cause the bias in illumina sequences? Thanks Mali