single end seq

[ariannigna]

Hello from London!
I'm planning a project of whole exome sequencing on human samples.
We bought the 2.1M Nimblegen array and are going to seq on GAII.
the library is based on a single end sequencing
I have to decide the read lenght with the GAII but I don't understand how it'll affect the coverage.
With a single end is it better to have short (36bp) or long (75bp)read lenght?

[Xi Wang]

Hello from London!
I'm planning a project of whole exome sequencing on human samples.
We bought the 2.1M Nimblegen array and are going to seq on GAII.
the library is based on a single end sequencing
I have to decide the read lenght with the GAII but I don't understand how it'll affect the coverage.
With a single end is it better to have short (36bp) or long (75bp)read lenght?

The mappability of short reads and long reads are different. Longer reads will have more percentage of reads that can be uniquely mapped to the reference genome.

[ariannigna]

thanks for you reply.
so if I decide to go for the single end seq and a short read lenght I should end up with higher coverage ... but higher chance to miss indels and duplication?

[Xi Wang]

When a short read map back to the reference genome, there would be more than one loci that the short read hits. This is due to the sequence repeat of a genome. Also you can refer to the UCSC track "mappability":

http://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=150896136&c=chrX&g=wgEncodeMapability