Dear All,
I am running cisgenome to identify known motif mapping of chipseq TF data on Windows GUI. Using one motif matrix and mm9 mouse Genome data base, If i run cisgenome for known motif mapping with Single Matrix-COD procedure. there are no errors/warnings at all, but also no output(if it works well. it should be run for a while. but for my running. it stops very quickly(guessing something wrong although, there is no error). So. i checked out my cod file which i manually converted from my bed file. It seems in the cod file, there is a problem because, all start sites of chr are zero and strand information all is plus. (I converted my bed file into cod file using file_bed2cod function of cisgenome in command line.) And in .ini file, path looks right. does not contain space.
Please see below my bed file and cod file for top 20 lines, respectively.
##my bed file.
chr14 59135524 59135706
chrX 1.66E+08 1.66E+08
chr10 1.16E+08 1.16E+08
chr4 1.37E+08 1.37E+08
chr11 96270051 96270214
chr9 35281744 35281907
chr6 21950204 21950350
chr17 30390087 30390246
chr8 91936049 91936211
chr6 1.01E+08 1.01E+08
chr3 8717560 8717788
chr1 72356341 72356559
chr6 99863120 99863308
chrX 1.09E+08 1.09E+08
chr4 9148012 9148160
chr11 35490303 35490483
chr17 26191518 26191660
chr10 1.23E+08 1.23E+08
chr19 10391552 10391688
chr5 33284156 33284326
###my cod file after i converted bed file into using file_bed2cod.
#seq_id chromosome start end strand
chr14 0 59135524 +
chrX 0 1.66E+08 +
chr10 0 1.16E+08 +
chr4 0 1.37E+08 +
chr11 0 96270051 +
chr9 0 35281744 +
chr6 0 21950204 +
chr17 0 30390087 +
chr8 0 91936049 +
chr6 0 1.01E+08 +
chr3 0 8717560 +
chr1 0 72356341 +
chr6 0 99863120 +
chrX 0 1.09E+08 +
chr4 0 9148012 +
chr11 0 35490303 +
chr17 0 26191518 +
chr10 0 1.23E+08 +
chr19 0 10391552 +
chr5 0 33284156 +
any thoughts? I missed something here?
Your inputs will be very helpful,
I am running cisgenome to identify known motif mapping of chipseq TF data on Windows GUI. Using one motif matrix and mm9 mouse Genome data base, If i run cisgenome for known motif mapping with Single Matrix-COD procedure. there are no errors/warnings at all, but also no output(if it works well. it should be run for a while. but for my running. it stops very quickly(guessing something wrong although, there is no error). So. i checked out my cod file which i manually converted from my bed file. It seems in the cod file, there is a problem because, all start sites of chr are zero and strand information all is plus. (I converted my bed file into cod file using file_bed2cod function of cisgenome in command line.) And in .ini file, path looks right. does not contain space.
Please see below my bed file and cod file for top 20 lines, respectively.
##my bed file.
chr14 59135524 59135706
chrX 1.66E+08 1.66E+08
chr10 1.16E+08 1.16E+08
chr4 1.37E+08 1.37E+08
chr11 96270051 96270214
chr9 35281744 35281907
chr6 21950204 21950350
chr17 30390087 30390246
chr8 91936049 91936211
chr6 1.01E+08 1.01E+08
chr3 8717560 8717788
chr1 72356341 72356559
chr6 99863120 99863308
chrX 1.09E+08 1.09E+08
chr4 9148012 9148160
chr11 35490303 35490483
chr17 26191518 26191660
chr10 1.23E+08 1.23E+08
chr19 10391552 10391688
chr5 33284156 33284326
###my cod file after i converted bed file into using file_bed2cod.
#seq_id chromosome start end strand
chr14 0 59135524 +
chrX 0 1.66E+08 +
chr10 0 1.16E+08 +
chr4 0 1.37E+08 +
chr11 0 96270051 +
chr9 0 35281744 +
chr6 0 21950204 +
chr17 0 30390087 +
chr8 0 91936049 +
chr6 0 1.01E+08 +
chr3 0 8717560 +
chr1 0 72356341 +
chr6 0 99863120 +
chrX 0 1.09E+08 +
chr4 0 9148012 +
chr11 0 35490303 +
chr17 0 26191518 +
chr10 0 1.23E+08 +
chr19 0 10391552 +
chr5 0 33284156 +
any thoughts? I missed something here?
Your inputs will be very helpful,