Hi All
One of my lab bench colleagues is working on a constructing an Illumina mate pair library intended for use in a target capture procedure where a substantial amount of DNA is needed. Unfortunately, if she does size selection on this library she loses 90+% of her library and so she is wondering what the consequences of not doing the size selection will have on de novo assembly using this library. I believe she is attempting to make a 6kb insert library but but the size of the fragments varies from ~3-10kb. I would probably try to assemble this data (with short insert paired end data as well) using velvet but don't have much experience with mate pair libraries. Can anyone comment as to how detrimental this level of insert size variation would be in a velvet assembly or make suggestions how to deal with it?
Thanks
Mark
One of my lab bench colleagues is working on a constructing an Illumina mate pair library intended for use in a target capture procedure where a substantial amount of DNA is needed. Unfortunately, if she does size selection on this library she loses 90+% of her library and so she is wondering what the consequences of not doing the size selection will have on de novo assembly using this library. I believe she is attempting to make a 6kb insert library but but the size of the fragments varies from ~3-10kb. I would probably try to assemble this data (with short insert paired end data as well) using velvet but don't have much experience with mate pair libraries. Can anyone comment as to how detrimental this level of insert size variation would be in a velvet assembly or make suggestions how to deal with it?
Thanks
Mark
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