Hi,

I am trying to use the MEDIPS package for one cfMeDIP-seq dataset. I only have the BEDPE file, which MEDIPS doesn’t accept as input in paired-end mode. I am thinking to convert the BEDPE to BED by taking the ‘samll’ start and ‘large’ end such that the read covers both original reads and use this as input to MEDIPS (such as createSet function).

For example, from

chr14   71752555    71752651    chr14   71752602    71752698    .   .   +   -
chr6    118605756   118605832   chr6    118605756   118605832   .   .   -   +

to

chr14   71752555    71752698    .   .   +
chr6    118605756   118605832   .   .   -

Do you think that make sense? Do you have any recommendation what I could do in this case? I’d really appreciate your opinions.

Thank you!

Luomeng