annotations of the BEDPE files

Bogdan Tanasa

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Mar 9, 2021, 9:25:34 PM3/9/21

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Dear Aaron, and all,

i may have missed this piece of information in the documentation : would you please let me know how/if we could use BEDTOOLS to annotate BEDPE files (from HIC pipelines, eg JUICER), with the closest TSS (or enhancer, or other feature) to each anchor ? thanks,

-- bogdan

Aaron Quinlan

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Mar 15, 2021, 9:02:27 AM3/15/21

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Hi Bogdan,

Unfortunately, the “closest” tool only works for BED (not BEDPE) format. You could convert the BEDPE file to BED, compute closest for each end, then use groupby to combine the results for each anchor. Sorry there isn’t a cleaner way.

Take care,

Aaron

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Bogdan Tanasa

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Mar 15, 2021, 6:43:20 PM3/15/21

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Thank you for your message and confirmation, Aaron.

all the best wishes,

-- bogdan

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