We aim to use Nimblegen seqcap EZ choice library to target-sequence ~ 100 genes of interests including promoters, coding and intronic regions. NimbleDesign tool provides the information of the probes used for target enrichment. However, when I visualize the probe coverage under UCSC genome browser, several genes contain exons that will NOT be covered by the probes (i.e. gaps).
If I understand the principles of target enrichment correctly, as the sole purpose of the probes is to "enrich" the chromosome regions of interest and all chromosomes are first shattered to be ~500 bp to 1kb in length. Is it correct to assume that if the "uncovered" exons are only a few hundred bases away from the probes, the exons will still be enriched and we'll get the sequence of them.
Any insight to share will be greatly appreciated. Thank you
If I understand the principles of target enrichment correctly, as the sole purpose of the probes is to "enrich" the chromosome regions of interest and all chromosomes are first shattered to be ~500 bp to 1kb in length. Is it correct to assume that if the "uncovered" exons are only a few hundred bases away from the probes, the exons will still be enriched and we'll get the sequence of them.
Any insight to share will be greatly appreciated. Thank you
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