Table 3 shows a comparison of the new filters with the frequency score filter on various aspects.
Nan Leng at Illumina, Inc. provided the average quality score filtering script.
The performance of discontiguous MegaBLAST at all word sizes is clearly more specific than contiguous MegaBLAST when the latter is run with no score filtering at all.
For instance, one can choose to lower the Q score filtering criteria, loosen the adapter detection perfect-match, or decrease the size selection range.
They were then subjected to an intensity score filtering with a cut-off of 20 fluorescence units (Supplementary Tables S1 [upregulated, 418] and S2 [downregulated, 364]).
word size 11, with no score filtering word size of 11 with a match length of 21 using a discontiguous seed, with no score filtering Overall, for this particular comparison, the best parameters were short contiguous word size settings for MegaBLAST.
For instance, for D20 of the estrous cycle, number of reads, after applying phred quality score filtering [ 14] (phred score >20 for each base) was reduced from 6,605,189 to 3,210,430.
Application of read depth, density, and quality score filters with the Maq SNPFilter reduced the SNP count among the three GA2-derived transcriptomes to 575,340 SNPs (i.e., Filtered SNPs; Figure 2).
Finally, identical junctions are collapsed into a single junction and all junctions are scored, filtered by score, and divided by splice-site edges, with canonical (GT-AG and GC-AG) junctions in one result set and non-canonical edges in a second result set.
