Fwd: consult

[michael stevens]

Hello锟斤拷
I am a Chinese student and I am interested in the tool
"methylCRF".When I use command "methylCRF.pl ",it requires "
MRE_FRAGMENT CpG's sampled by MRE-seq. format: CpGid[0|1] where CpGid
corresponds to cpg.bed.

"(http://methylcrf.wustl.edu/) , as the perl code said "$fragdir, # dir
with MRE enzyme frag files -will detect if it's instead a filename and
use that".And in that website,the file is "MRE_3enz_4_6000.bed.bin".I
want to know whether this file comes from the MRE-seq itself or we
process the datas from MRE-seq and get it ? If the latter,how can I get
this file using my own datas?Thanks.

[michael]

Hi,

Thanks for your interest in methylCRF.  Originally, I had the code generate the MRE enzyme frag files, but I now think it is not a robust approach.  I now generate them in a separate process.  I originally left the old code in methlCRF.pl in case I change my mind again.

Note that the enzyme file for MRE_norm.pl and methylCRF.pl are different.  The one for MRE_norm.pl is:
 wget http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_3enz_4_6000.bed

The one for methylCRF.pl is at:
http://methylcrf.wustl.edu/hg19/MRE_frags/MRE_3enz_4_6000_cpg.bin

I know this is sub-optimal, and as with the code mentioned above, I will change it in the future when I get some time.

I hope this helps.  Please ask if anything isn't clear.