error in the output of bedops

Question

[María José]

Hi,

I've encountering issues with bedtools intersect. However, I think the problem reside in bedops which has been used to find common genomic regions across samples. However, it encountered an error.

bedops -m c1_macs3 u2_macs3 c3_macs3 u4_macs3 > merged_peaks.bed 
bedtools intersect -a merged_peaks.bed -b u1_macs3 -wa > common_u1.bed

Error: unable to open file or unable to determine types for file merged_peaks.bed

- Please ensure that your file is TAB delimited (e.g., cat -t FILE).
- Also ensure that your file has integer chromosome coordinates in the expected columns (e.g., cols 2 and 3 for BED).

I suspect the problem lies in the file obtained from BEDOPS. The header contains some incorrect entries, such as a genomic position labeled with "hr1":

track   1   0
ype=narrowPeak  1   0
ame="u2_macs3"  1   0
ame="u4_macs3"  1   0
ame="c1_macs3"  1   0
ame="c3_macs3"  1   0
escription="u2_macs3"   1   0
escription="u4_macs3"   1   0
escription="c1_macs3"   1   0
escription="c3_macs3"   1   0
extItemButton=on    1   0
hr1 9950    10800

Any insight in this topic would be greatly appreciated.

Answer 1

[GenoMax]

Can you show what is in the *macs* files?

You should also try adding --header flag to your bedops command since it appears to be mangled in the output you show (first character is missing in all lines).

Edit: Based on the response from @Alex adding the --header option to the bedops command is the solution.

[María José]

Hi, it is the output of macs3 bdgpeakcall module. Ex: chr1 2124150 2124400 c3_macs3_narrowPeak3 170 . 0 0 075

[Alex Reynolds]

https://github.com/bedops/bedops/issues/287#issuecomment-2904811765