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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.