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An example of the coverage of one of the target genes as well as the positions of the probes and the repeat elements in both types of libraries is shown in Figure 2. We obtained average sequence depths of 59 to 101 for the Nimblegen libraries and 86 to 113 for the SureSelect libraries after downsampling (Table 2).
We compared the HapMap genotypes and the genotypes obtained by sequencing from both types of libraries in all the positions where the sequencing call obtained with either method disagreed with the HapMap genotype in order to look for allelic drop outs.
This indicates that to approach full transcriptome information, the sequencing of both types of libraries is necessary.
Numbers of transcripts assigned to each neural process are shown, including numbers assembled from embryo library sequences only, from CNS libraries only, and from a mix of ESTs from both types of libraries.
The correlation between same stages in different data sets (PA and RZ), while moderate, is highly significant (p ≤10−15), reflecting the representation of most transcripts in both types of libraries.
Both types of libraries contain sequenced genomic fragments that are effectively randomly distributed throughout the genome; however, they differ in being comprised of actively transcribed components only in the case of EST libraries versus random genomic fragments in the case of BAC libraries.
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Therefore, it was advantageous to our project to make both types of library, preserving in some cases the natural transcript ratios present in the source tissues, and in others bringing the representation of housekeeping genes more in line with that of rarely expressed transcripts.
Our SNP calls from both types of sequencing libraries correlated very well with the HapMap genotypes on the individual level reflecting the high quality of the SNP calls.
The transcriptomes revealed by MPSS and SBS had a high correlation co-efficient (0.81 to 0.90), and about 70% of the transcripts were commonly identified in both types of the libraries.
We discuss details of coverage and filtering results for both types of long-insert linking libraries in the Results.
There are two types of libraries on campus: The University Library system and the Affiliated Libraries.
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