error with number of fields in bedtools

Question

[aishwaryamandava7]

I have two files, file A and file B. File A looks like this

3R  26969363  26969744  
3R  27596423  27598953  
3R  27596424  27597575  
3R  27598277  27598952  
3R 27598951   27601828  
3R 27601079   27601205    
4  44758        45814  
4  44758        45814  
4  329255      329453  
4  547084      548882

File B looks like this:

3R      27446370        27448445        Unspecified_VT48351  
3R      27449778        27452027        Unspecified_VT48353  
3R      27451198        27451698        Unspecified_STARR-OSC-3001  
3R      27455002        27457116        Unspecified_VT48356  
3R      27462241        27462741        Unspecified_STARR-OSC-1147  
3R      27504391        27504891        Unspecified_STARR-OSC-3255  
3R      27505415        27505915        Unspecified_STARR-S2-4346  
3R      27556636        27557136        Unspecified_STARR-OSC-2452  
3R      27566429        27568568        Unspecified_VT48413  
3R      27569900        27571995        Unspecified_VT48415  
3R      27570524        27571024        Unspecified_STARR-OSC-1831  
3R      27570564        27571064        Unspecified_STARR-S2-2753  
3R      27571446        27573714        Unspecified_VT48416  
3R      27574983        27577188        Unspecified_VT48418

I need to remove the overlapping regions from file B, so that file B no longer has overlapping regions of file A. I used bedtools subtract for this.

bedtools subtract -a fileb -b filea

it threw an error: line number 5 of filea has 4 fields, but three were expected. But the file has only three columns. Both the files, filea and fileb are tab-delimited

[Carlo Yague]

Have you checked that there is no "invisible" tabulation at the end of some lines of filea (such as line 5) ?

Answer 1

[Alex Reynolds]

You could try bedops:

$ bedops --not-element-of -1 B.bed A.bed > answer.bed