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Comparing bed files for shifts and enlargements

I was wondering how I can analyze the changes in two different bed files such as:

  1. Shifts (if start-end shifted from, for example, 10-20 to 15-25
  2. Enlargements (if start-end shifted from, for example, 10-20 to 5-25) 2.a and in which direction (did it enlarge both directions or only single)
  3. Shrinkage (if start-end shifted from, for example, 10-20 to 12-18)

Any help would be very appreciated. Thank you so much!

bed bedtools chip-seq
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written by Deniz • Deniz

id assume you want to visualize them?

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written by LauferVA LauferVA

Do you want to compare the first entry of the first file with the first entry in the second file, the second with the second, and so on?

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written by Malcolm.Cook Malcolm.Cook

I want to compare all the entries to each other (more like a double for loop)

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written by Deniz • Deniz

1 answer

If you're aiming to visualize differences, you could throw datasets into a HiGlass viewer and lock two tracks (one "control", the other "treatment"). Then browse your regions of interest.

Otherwise, you could pipe bedmap to awk to measure offsets, percentage or fold differences between elements between tracks. Spit the values out to to a text file and then feed that into R to summarize and visualize statistics.

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written by Alex Reynolds Alex Reynolds

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