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Old 04-04-2013, 08:37 AM   #1
halo_ox
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Location: Oxford

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Default mergeBed -scores help

Hi,

I am attempting to run mergeBed on a bed file with 4 columns: chr start end and fold_enrichment FDR(%).

I wish to merge intervals which are within 100bp and keep the max FDR score associated with the interval. When I run the following command:

mergeBed -scores max -d 100 -i input.bed > output.bed

I get the following error:

*****
*****ERROR: No scores found to report for the -scores option. Exiting.
*****

The output file has one row containing only a chr, start and end (no FDR).

Any advice of how to get this command to work would be gratefully received : )

Thank you.
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Old 04-04-2013, 08:47 AM   #2
rjohnp
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Default

Hi,

the issue is that the 'score' must be column 5, you have it in 4. From https://genome.ucsc.edu/FAQ/FAQformat.html:

Quote:
BED format provides a flexible way to define the data lines that are displayed in an annotation track. BED lines have three required fields and nine additional optional fields. The number of fields per line must be consistent throughout any single set of data in an annotation track. The order of the optional fields is binding: lower-numbered fields must always be populated if higher-numbered fields are used.
If you just insert a 4th column with a name prior to the score column (easy in Awk if you're using Linux) then it should work.

Hope that helps.
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Old 04-04-2013, 08:48 AM   #3
halo_ox
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Thank you for such a quick and helpful reply! : )
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Old 04-04-2013, 09:00 AM   #4
halo_ox
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That has worked. Thank you : D
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