4Cseqpipe for long-range interaction

Question

[ta_awwad]

Dear All, I am trying to analyse 4C-seq library with 4Cseqpipe program. the program allows to generate genome fragments from a binary ".seq" format .. I have no idea how generate such file for mm10 using fasta file .. does anyone know how to do this.. many many thanks

[ATpoint]

From what I understand, these files are created as part of the pipeline:

perl 4cseqpipe.pl –build_re_db –first_cutter XXXX –second_cutters YYYY [,ZZZZ] -trackdb_root root_directory

See the manual. Does that command work for you?

[ta_awwad]

the files are only for mm9 coordinates ... i was wondering if one could do it for mm10 .. second I still don't get what root_directory here means actually