I found a problem when using your software, which is that when I use the BatMeth2 methyGff function, I cannot obtain the methylation annotation file downstream of the gene，cause i can not find the parameter to generate this . and i want to get the result like this:
downstream_chrom downstream_regionStart downstream_strand downstream_context C_count downstream_CT_count downstream_regionID
ex. Chr1 3631 + CG 45 1314 AT1G01010
DNA methylation level distributions in body and -bp flanking sequences. The distance of upstream and downstream. default:2000
-B/--body
Calculate the DNA methylation level of per region.
-P/--promoter
Calculate the DNA methylation level of per region's upstream [d]k.
--TSS
Caculate matrix for TSS. [Outfile: outPrefix.TSS.cg.txt]
--TTS
Caculate matrix for TTS. [Outfile: outPrefix.TTS.cg.n.txt]
--GENE
Caculate matrix for TSS. [Outfile: outPrefix.TSS.cg.txt]
--TTS
Caculate matrix for GENE and flank [d]k. [outPrefix.GENE.cg.txt]
-s/--step
Gene body and their flanking sequences using an overlapping sliding window of 2% of the sequence length at a step of 1% of the sequence length. So default step: 0.01 (1%)
-bl/--bodyLen
Body length to which all regions will be fit. (default: same as -d)
-S/--chromStep
Caculate the density of genes/TEs in chromsome using an overlapping sliding window of 100000bp at a step of 50000bp, must equal "-s" in Split.. default step: 50000(bp)
--help/-h
Print help
But this result is quite important for my analysis. Do you have any corresponding scripts to implement this function?
I hope you can reply to my request in your busy schedule. Thank you very much
I found a problem when using your software, which is that when I use the BatMeth2 methyGff function, I cannot obtain the methylation annotation file downstream of the gene，cause i can not find the parameter to generate this . and i want to get the result like this: downstream_chrom downstream_regionStart downstream_strand downstream_context C_count downstream_CT_count downstream_regionID
ex. Chr1 3631 + CG 45 1314 AT1G01010
DNA methylation level distributions in body and-bp flanking sequences. The distance of upstream and downstream. default:2000
-B/--body
Calculate the DNA methylation level of per region.
-P/--promoter
Calculate the DNA methylation level of per region's upstream [d]k.
--TSS
Caculate matrix for TSS. [Outfile: outPrefix.TSS.cg.txt]
--TTS
Caculate matrix for TTS. [Outfile: outPrefix.TTS.cg.n.txt]
--GENE
Caculate matrix for TSS. [Outfile: outPrefix.TSS.cg.txt]
--TTS
Caculate matrix for GENE and flank [d]k. [outPrefix.GENE.cg.txt]
-s/--step
Gene body and their flanking sequences using an overlapping sliding window of 2% of the sequence length at a step of 1% of the sequence length. So default step: 0.01 (1%)
-bl/--bodyLen
Body length to which all regions will be fit. (default: same as -d)
-S/--chromStep
Caculate the density of genes/TEs in chromsome using an overlapping sliding window of 100000bp at a step of 50000bp, must equal "-s" in Split.. default step: 50000(bp)
--help/-h
Print help
But this result is quite important for my analysis. Do you have any corresponding scripts to implement this function? I hope you can reply to my request in your busy schedule. Thank you very much