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.
•
written
by
María José •
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.
Hi, it is the output of macs3 bdgpeakcall module. Ex: chr1 2124150 2124400 c3_macs3_narrowPeak3 170 . 0 0 075
Log in to answer this question.