Intersecting multiple bed files

[asapp]

Hello,

I have several RNA-Seq transcript data sets assembled and in BED format. I have masked out previously identified transcripts from the data, leaving me with "unidentified" transcripts. A visual of this data in the UCSC Genome Browser is attached.

I need to computationally gather the locations where all of the resulting transcripts intersect. In looking though the bedtools intersect function, it seems that there is no option to specify regions where ALL the files intersect, only those where at least 2 of the supplied files intersect.

Have any of you encountered this issue before? What are your suggested workarounds? Would I need to continually compare 2 files and then keep comparing that output to the next file and so on? Or is there an option I am unaware of/another software function that can handle this?

Thank you all very much!
-Anna

[blancha]

bedops --intersect first.bed second.bed third.bed > result.bed

https://bedops.readthedocs.org/en/latest/content/reference/set-operations/bedops.html#intersect-i-intersect

[asapp]

Perfect, thanks!