Average insert size of PE library based on the bioanalyzer results

Question

[seta]

Hi friends,

Please help me about the average insert size for paired end library (100bp) made by dUTP method on Illumina platform. The sequencing center told us “from the bioanalyzer results, the cDNA fragment have been cut targeting approximately 160 bp usually the standard deviation is approximately 40bp”. Could you please help me to correctly know the average insert size?

I adjusted the size of 200 bp for SOAP-de novo-trans assembler, but since too much contig remained as singletons (don’t located in the scaffold), I’m in a doubt for right average insert size. Thank you for any comments and suggestion.

[Irsan]

If you want to emperically define the insert sizes then map your reads back to your contigs and use that alignment to get your insert sizes. Otherwise, use the values provided by your seq provider (those values include the read lengths! Dont know if that is how insert sizes should be defined for soap)

Answer 1

[h.mon]

As Irsan pointed out, you may map your reads on your contigs and estimate insert size - BBMap has an "ihist=" option to save a histogram of insert size calculated from mapping.

You may also merge the paired reads and estimate the insert size - BBMerge has an "ihist=" option to save a histogram of insert size calculated from the merged pairs. Note that this will underestimate insert size, as only merged read pairs will be used on the calculation.