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Table 5 Read filtering for differences in library preparation

From: Impact of sequencing depth and technology on de novo RNA-Seq assembly

  Preprocessing
Platform Name Raw Filtered Mapped Deduplicated
DNBseq™ ERR1831362 48 148 821 45 828 900 44 015 469 32 497 907
ERR1831363 29 782 959 28 352 783 27 237 354 21 102 998
ERR1831364 54 940 056 52 466 727 50 421 993 36 693 200
ERR1831365 36 073 210 34 329 221 32 932 438 24 745 818
ERR1831366 43 664 065 41 782 043 40 108 615 29 250 048
ERR1831367 55 025 946 52 410 892 50 302 197 36 153 502
ERR1831368 53 296 161 50 698 009 48 688 107 34 475 744
ERR1831369 65 455 754 62 428 710 59 984 288 41 622 545
ERR1831370 29 774 053 28 307 062 27 164 676 20 606 457
HiSeq SRR1261168 134 921 154 104 132 308 101 903 998 70 430 950
SRR1261170 72 897 482 33 367 214 32 597 422 27 498 074
SRR950078 100 387 010 77 761 236 73 979 293 50 505 406
SRR950080 91 781 477 69 875 633 66 896 955 49 310 706
SRR950084 125 083 194 93 367 543 89 192 069 61 653 799
DNBseq™ Total 416 161 025 396 604 347 380 855 137 277 148 219
% Removed   4.70% 3.97% 27.23%
HiSeq Total 525 070 317 378 503 934 364 569 737 259 398 935
% Removed   27.91% 3.68% 28.85%
  1. Here we show reads remaining after each preprocessing step. The columns indicate read counts after SOAPnuke filtering (Filtered), aligning to GRCh38 with HISAT2 (Mapped), and PCR deduplication with Picard Tools (Deduplicated)