Hello everyone!
I’m up to generate an Ilumina Mate pair library to scaffold earlier de novo sequence data. But know I have the agony of choice what fragment size to use. The manufactures protocol provides a variation in fragment sizes from 2-5kb, but I’m not really sure about the pros and cons of shorter or longer fragment sizes.
Is it only a question of the expected repeat lengths I’d like to span within a given genome? If this is the case, its "more or less" always better to choose larger fragment/gap sizes isn't it
Maybe anybody has some experiences, if scaling up/down fragment sizes has negative/positive effects on the library’s quality?
I mean like diversity, total amount or chimeric artifacts of the reads?
Thanks a lot for you efforts!!!
Rob
I’m up to generate an Ilumina Mate pair library to scaffold earlier de novo sequence data. But know I have the agony of choice what fragment size to use. The manufactures protocol provides a variation in fragment sizes from 2-5kb, but I’m not really sure about the pros and cons of shorter or longer fragment sizes.
Is it only a question of the expected repeat lengths I’d like to span within a given genome? If this is the case, its "more or less" always better to choose larger fragment/gap sizes isn't it
Maybe anybody has some experiences, if scaling up/down fragment sizes has negative/positive effects on the library’s quality?
I mean like diversity, total amount or chimeric artifacts of the reads?
Thanks a lot for you efforts!!!
Rob