I have a library that I am running on a HiSeq2000 for PE-100 reads. The fragment sizes range from 150bp to 1.3kb. I can't do much about this range since we are PCR capturing unknown regions using inverse PCR. The majority of the fragments sit in the 500bp range, but will having this wide of a range affect clustering/sequence quality/number of reads? Will there be a bais away from the larger fragments?
Thanks.
Thanks.
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