Author: Pandya, Gagan A.; Holmes, Michael H.; Sunkara, Sirisha; Sparks, Andrew; Bai, Yun; Verratti, Kathleen; Saeed, Kelly; Venepally, Pratap; Jarrahi, Behnam; Fleischmann, Robert D.; Peterson, Scott N.
Title: A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform Document date: 2007_11_15
ID: 16tii0ha_33
Snippet: The raw resequencing data (N = 2) for both the LVS and the SCHU S4 strains, using Affymetrix data processing methods, are shown in Table 2 . These results used a call rate cutoff value of zero. The recommended value of 0.5 is appropriate in cases where the samples in the batch are highly homogeneous. In our case, the batch was chosen for maximum diversity, and an arbitrary requirement of some minimum fraction of calls across the batch would have .....
Document: The raw resequencing data (N = 2) for both the LVS and the SCHU S4 strains, using Affymetrix data processing methods, are shown in Table 2 . These results used a call rate cutoff value of zero. The recommended value of 0.5 is appropriate in cases where the samples in the batch are highly homogeneous. In our case, the batch was chosen for maximum diversity, and an arbitrary requirement of some minimum fraction of calls across the batch would have resulted in unnecessary loss of data at many locations in the query sample. The results in Table 2 illustrate that the performance of the platform was dependent on the similarity between the query genome and the reference content of the resequencing chip. The number of miscalled bases for SCHU S4 was larger than that observed for LVS; however, the raw data still apparently had a good overall call rate and base-calling efficiency.
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