D prices of WBSA with BSMAP and Bismark. The results show
D rates of WBSA with BSMAP and Bismark. The results show that mapped rates or uniquely mapped rates of WBSA have been superior to that of BSMAP. The uniquely mapped rates of Bismark had been the highest for thePLOS One particular | plosone.orgTable 4. Comparison of mapping times and accuracies amongst WBSA, BSMAP, and Bismark for simulated WGBS information.Study length (bp) Species Alignment Parameters Num. (pairs) -q hred33-quals -n three -l 16 -s 16 -v three -p 1 -r 1 -R -u -n three -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 3 -l 16 -s 16 -v three -p 1 -r 1 -R -u -n three -l 16 -k three -q hred33-quals -n three -l 16 -s 16 -v 3 -p 1 -r 1 -R -u -n 3 -l 16 -k 3 -q hred33-quals -n two -l 14 -s 14 -v two -p 1 -r 1 -R -u -n two -l 14 -k 2 -q hred33-quals -n two -l 14 -s 14 -v two -p 1 -r 1 -R -u -n two -l 14 -k 2 three.94 ,1.1 0.77 ,1.7 23412528 23442168 9.53 ,1.five 21158772 15.93 ,four.3 84786571 eight.05 ,4.3 84242377 94.36 94.97 85.74 94.87 94.99 39.77 ,five.1 77325014 86.61 4.92 ,1.two 23442166 94.99 1.03 ,1.eight 23422665 94.92 ten.72 ,1.2 21390366 86.68 21034061 19760196 23121395 76000508 70017299 84068061 20741988 19161765 22910455 25.45 ,four.three 84786567 94.97 84697662 11.45 ,four.3 84383101 94.52 ErbB3/HER3 Inhibitor site 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 ,1.2 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 ,1.5 21570946 87.41 21266096 86.18 0 24.07 ,4.3 84,776,394 94.96 80,698,421 90.39 0 7.60 ,four.three 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 ,5.5 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 Damaging Num. (pairs) five,985,422 347,016 10,178 1871224 25559 8 6626175 403471 five 2051804 19505 4 7461558 544228 1 2283398 29642 2 six.70 0.39 0.01 7.58 0.10 0 7.42 0.45 0 eight.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.eight.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 Bisulfite Sequence AnalysisWeb-Based Bisulfite Sequence AnalysisTable five. Comparison of mapping times and accuracies between WBSA, BSMAP, and Bismark for simulated RRBS data.SpeciesSoftwareAlignment ParametersMapping Time (hours)RAM (Gb)Mapped Reads Num. 67.63 94.58 94.97 68.three 94.52 94.Properly Mapped Reads Num. 10849359 12489088 12302379 5065633 5603328 5594941 67.13 73.09 72.00 67.87 75.08 74.False Optimistic Num. 795 23 264 206 five 51 0 0 0 0.06 0 0.False Unfavorable Num. 5303277 71662 5286 1990768 36064 2537 31.04 0.42 0.03 26.67 0.48 0.HumanBismark (v0.eight.1) BSMAP (v2.74) WBSA-q hred33quals -n two -l 14 -s 14 -v 2 -p 1 -r 1 -R -u -n two -l 14 -k 2 -q hred33quals -n 2 -l 14 -s 14 -v 2 -p 1 -r 1 -R -u -n two -l 14 -k5.54 1.22 1.42 1.52 0.28 0.,10.five ,7.five ,6.3 ,7.1 ,six.8 ,6.IL-15 Inhibitor review 10930929 16161772 16228389 5099599 7054102MouseBismark (v0.8.1) BSMAP (v2.74) WBSAdoi:ten.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 between those of BSMAP and Bismark (Table 6). Thinking about all of the above outcomes, we conclude that the WBSA mapping approach was a lot more correct and effective than the other two techniques.2) Evaluatio.
