error with number of fields in bedtools
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
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Alex Reynolds
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aishwaryamandava7 •
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aishwaryamandava7 •
1 answer
You could try bedops:
$ bedops --not-element-of -1 B.bed A.bed > answer.bed
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Have you checked that there is no "invisible" tabulation at the end of some lines of filea (such as line 5) ?