. 2015 Aug 9;14(Suppl 2):235–245. doi: 10.4137/CIN.S17286

Table 3.

The description of HMPL Part II (Parse.HMPL.pl) output files.

FILE NAME	CONTENTS
^*.grX eg, MCF10A.gr5	The C_pG sites with coverage greater than X (X > 0).
^*.all.HM.sites eg, MCF10A.gr5.all.HM.sites	The hemimethylated C_pG sites identified by the high and low cutoff values.
^*.all.HM.sites.annotated eg, MCF10A.gr5.all.HM.sites.annotated	The annotated hemimethylated sites (ie, gene names are provided).
^*.all.labelled.CG eg, MCF10A.gr5.all.labelled.CG	The C_pG sites with coverage greater than X and with the labels of methylation states (P: partially methylated, M: methylated, U: unmethylated).
^*. Summary eg, MCF10A.gr5.summary	The summary file for all the methylation states of single hemimethylation sites and clusters.
^*.all.HMClusters eg, MCF10A.gr5.all.HM.Clusters	All hemimethylated clusters.
^*.all.Rev.Clusters eg, MCF10A.gr5.all.Rev.Clusters	All of the polarity (or reverse) clusters, including both consecutive and non-consecutive polarity clusters.
^*.non.Rev.Clusters eg, MCF10A.gr5.non.Rev.Clusters	The hemimethylated clusters that are not polarity patterns.
^*.Singleton eg, MCF10A.gr5.Singleton	Single hemimethylated C_pG sites.
^*.consec.revs.Clusters eg, MCF10A.gr5.consec.revs.Clusters	The consecutive polarity (or reverse) clusters (ie, with just two consecutive C_pG sites).
^*.non.consec.revs.Clusters eg, MCF10A.gr5.non.consec.revs.Clusters	The non-consecutive polarity clusters (ie, with two C_pG sites that are not consecutive).
^*.compare eg, MM.gr5.all.HM.sites.annotated.compare MM.gr5.consec.revs.Clusters.compare MM.gr5.non.consec.revs.Clusters.compare MM.non.Rev.Clusters.compare MM.gr5.Singleton.compare	The results of comparing two samples. (Note: To save space, we use “MM” to denote “MCF10A.MCF7” for the file names in the left column).