Gnment Parameters Num. (pairs) -q hred33-quals -n three -l 16 -s 16 -v three -p 1 -r 1 -R -u -n 3 -l 16 -k three -q hred33-quals -n 3 -l 16 -s 16 -v three -p 1 -r 1 -R -u -n 3 -l 16 -k 3 -q hred33-quals -n three -l 16 -s 16 -v 3 -p 1 -r 1 -R -u -n three -l 16 -k three -q hred33-quals -n three -l 16 -s 16 -v three -p 1 -r 1 -R -u -n 3 -l 16 -k three -q hred33-quals -n two -l 14 -s 14 -v 2 -p 1 -r 1 -R -u -n two -l 14 -k 2 -q hred33-quals -n 2 -l 14 -s 14 -v two -p 1 -r 1 -R -u -n two -l 14 -k two 3.94 ,1.1 0.77 ,1.7 23412528 23442168 9.53 ,1.five 21158772 15.93 ,4.3 84786571 8.05 ,four.three 84242377 94.36 94.97 85.74 94.87 94.99 39.77 ,5.1 77325014 86.61 4.92 ,1.2 23442166 94.99 1.03 ,1.eight Caspase 4 Formulation 23422665 94.92 ten.72 ,1.two 21390366 86.68 21034061 19760196 23121395 76000508 70017299 84068061 20741988 19161765 22910455 25.45 ,four.three 84786567 94.97 84697662 11.45 ,4.three 84383101 94.52 72790003 40.37 ,four.3 78160397 87.55 77067467 86.32 81.53 94.87 85.24 80.07 93.69 85.13 78.43 94.16 84.05 77.65 92.84 five.47 ,1.two 23442162 94.99 23289124 94.37 1.18 ,1.7 23416611 94.89 20235903 82.00 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12.57 ,1.five 21570946 87.41 21266096 86.18 0 24.07 ,four.three 84,776,394 94.96 80,698,421 90.39 0 7.60 ,four.3 84,439,556 94.58 70,308,940 78.75 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 47.80 ,five.5 78,801,150 88.26 77,891,346 87.25 0 0 Num. (pairs) Num. (pairs) Mapped Reads False PositiveSoftwareMapping Time (hours)RAM (Gb)Correctly Mapped ReadsFalse Adverse Num. (pairs) five,985,422 347,016 ten,178 1871224 25559 eight 6626175 403471 five 2051804 19505 four 7461558 544228 1 2283398 29642 2 six.70 0.39 0.01 7.58 0.ten 0 7.42 0.45 0 8.31 0.08 0 8.36 0.61 0 9.25 0.12PLOS One | plosone.orgZebrafish Bismark (v0.8.1)BSMAP (v2.74)WBSARiceBismark (v0.8.1)BSMAP (v2.74)WBSAZebrafish Bismark (v0.eight.1)BSMAP (v2.74)WBSARiceBismark (v0.8.1)BSMAP (v2.74)WBSAZebrafish Bismark (v0.eight.1)BSMAP (v2.74)WBSARiceBismark (v0.8.1)BSMAP (v2.74)WBSAdoi:ten.1371/journal.pone.0086707.tWeb-Based SSTR3 Species Bisulfite Sequence AnalysisWeb-Based Bisulfite Sequence AnalysisTable five. Comparison of mapping instances and accuracies amongst WBSA, BSMAP, and Bismark for simulated RRBS information.SpeciesSoftwareAlignment ParametersMapping Time (hours)RAM (Gb)Mapped Reads Num. 67.63 94.58 94.97 68.three 94.52 94.Appropriately Mapped Reads Num. 10849359 12489088 12302379 5065633 5603328 5594941 67.13 73.09 72.00 67.87 75.08 74.False Good Num. 795 23 264 206 5 51 0 0 0 0.06 0 0.False Negative Num. 5303277 71662 5286 1990768 36064 2537 31.04 0.42 0.03 26.67 0.48 0.HumanBismark (v0.8.1) BSMAP (v2.74) WBSA-q hred33quals -n 2 -l 14 -s 14 -v 2 -p 1 -r 1 -R -u -n two -l 14 -k two -q hred33quals -n 2 -l 14 -s 14 -v 2 -p 1 -r 1 -R -u -n 2 -l 14 -k5.54 1.22 1.42 1.52 0.28 0.,ten.five ,7.5 ,6.3 ,7.1 ,6.eight ,six.10930929 16161772 16228389 5099599 7054102MouseBismark (v0.8.1) BSMAP (v2.74) WBSAdoi:10.1371/journal.pone.0086707.tmouse dataset, but each rates have been not comparable with those of WBSA or BSMAP for the human dataset. The mapping time and memory use for WBSA fell amongst these of BSMAP and Bismark (Table six). Contemplating all the above final results, we conclude that the WBSA mapping process was extra accurate and effective than the other two strategies.two) Evaluation on the accuracy of WBSA analysisTo estimate the accuracies from the identification of methylation sites plus the advanced analysis benefits generated by WBSA, we downloaded the published embryonic stem cell dataset from the NCBI site (SRA accessions SRX006239?1, 1.12 G reads). The data are derived from the report of Lister et al. [10], who presented the f.
