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Table 2 Bioinformatics analysis pipeline for the identification of putatively methylated sites

From: Combined methylation mapping of 5mC and 5hmC during early embryonic stages in bovine

 

Blastocyst embryos

Elongation embryos

All

Method

Me-RDA

HMe-RDA

HELP cocktail

Me-RDA

HMe-RDA

HELP cocktail

 

Msp/Hpa

FspBI/BfaI

Msp/Hpa

FspBI/BfaI

Raw reads from library

313 330

179 105

242 864

208 963

94 961

243 874

1 283 097

Cleaned readsa

281 619

72 855

234 149

192 163

71 459

218 874

1 071 119

Validated readsb

N/A

N/A

46 835

N/A

N/A

50 462

N/A

Consensus sequencesc

33 123

29 416

31 604

25 616

24 963

41 784

186 506

Sequences with genomic alignmentsd

28 941

25 360

25 519

18 944

14 978

37 759

151 501

Sequences with unique alignmente

1890

11 772

14 712

1317

8858

30 587

69 136

Putative methylated restriction sitesf

3634

21 352

18 810

2584

15 714

39 367

101 461

  1. aNumber of reads left after cleaning with SeqClean. Reads smaller than 25 nt after adapter trimming were discarded. bFor HELP, number of reads with an internal HpaII, AciI or HinP1I restriction site. cNumber of consensus sequences after clustering with a 97% identity threshold. dNumber of consensus sequences with a BLAT genomic alignment with 92% identity over 92% of the length of the transcript. eNumber of consensus sequences for which a single alignment fits the above criteria. fNumber of potentially methylated sites identified in the genome through the alignment and extension of reads. N/A = not applicable.