# HG changeset patch # User eugen # Date 1345104810 14400 # Node ID 54492fec12ba298e4b3640bdf9672b7df4cea522 # Parent a2f7ecd6b4002544bd8254d2b705695c4a4e8daa Uploaded diff -r a2f7ecd6b400 -r 54492fec12ba bsmap_meth_caller.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bsmap_meth_caller.xml Thu Aug 16 04:13:30 2012 -0400 @@ -0,0 +1,59 @@ + + + + bsmap + + + + + samtools + + + + bsmap_meth_caller.sh + input=$bsmap_sam + unique=$unique + properly=$properly + zero_meth = $zero_meth + rem_dup = $rem_dup + combine_cpg = $combine_cpg + trimN = $trimN + depth = $depth + output=$output + tempdir=$output.files_path + ref="${ filter( lambda x: str( x[1] ) == str( $bsmap_sam.metadata.dbkey ), $__app__.tool_data_tables['bsmap_fasta'].get_fields() )[0][3] }" + + + + + + + + + + + + + + + +**What it does** + +This methylation caller parses the BSMAP SAM output file into bed format. + + +**Output format** :: + + + Column Description + ---------------------- -------------------------------------- + 1 chr chromosome + 2 pos position + 3 strand strand + 4 context context (CHH,CHG,CpG) + 5 coverage totally sequenced Cs at that position + 6 methylated methylated Cs at that position + 7 percentage methylated percentage of 6 + + +