Malformed BED entry at line 5. Start Coordinate detected that is < 0. Exiting.

Question

[dh]

I am trying to use the enrichment analysis in https://unibind.uio.no/ However, I ma having formatting issues with my BED file format and I keep getting the following error

Error: malformed BED entry at line 5. Start Coordinate detected that is < 0. Exiting.

I have checked my BED file and there is no issue with line 5. Se below an snippet of the BED file. Does anyone see where it is going wrong?

chr3    49020618    49020709
chr7    93483936    93484019
chr16   14303967    14304049
chr7    27169480    27169563
chr12   95308420    95308513
chrX    74287286    74287357
chr19   51693254    51693339
chr8    41660441    41660508
chr8    22244966    22245037
chr17   59137758    59137872
chr1    71067631    71067716
chr1    109598893   109598967
chr19   49500785    49500868
chr9    136670602   136670686
chr17   31559996    31560083
chr14   101054687   101054759
chr19   53697533    53697617
chr5    160485352   160485450
chr13   50048973    50049061
chr21   25573980    25574044
chr22   21653304    21653385
chr11   2134134 2134209
chr19   53666679    53666762
chr1    220117853   220117962
chr12   6963699 6963766
chr8    11035206    11035302
chr9    109046229   109046298
chr12   57519163    57519259
chrX    53556223    53556341
chr7    129770383   129770492
chr14   100884702   100884783
chr19   53701227    53701287
chr19   53713347    53713434
chr5    55170646    55170742
chr12   54337216    54337314
chr14   23417987    23418063
chr19   53702737    53702819
chr14   100911139   100911213
chr10   102436512   102436584
chr19   53690881    53690965
chr14   101065912   101065991
chr11   72615063    72615130
chr7    151238421   151238538
chrX    138667711   138667793
chrX    50014598    50014683
chr19   53679940    53680023
chrX    134170041   134170111
chr19   45638994    45639087
chr17   58331232    58331318
chr19   53787890    53787956
chr12   95308420    95308513
chr19   53686469    53686555
chrX    151959628   151959712
chr12   6964097 6964191
chr10   17845107    17845193
chr19   53731006    53731090
chr19   53698385    53698471
chr14   101065447   101065537
chr17   76736450    76736548
chrX    50008431    50008514
chr15   31065032    31065141

[cpad0112]

Please post data instead of data images.

[dh]

I have now posted the data instead of image. Thank you

[cpad0112]

can you sort bed file and feed to the server?

Answer 1

[Pierre Lindenbaum]

what is the output of

awk -F '\t' '(int($2)>int($3) || int($2)<0)' in.bed 

furthermore, try to remove the header chrom....

[Friederike]

Seconding this, my money would be on the header line not being commented out.

The error is usually an indication that the format of the BED file does not meet the expectations of BEDtools, most commonly because of inconsistent white spaces (the expectation is for tab-separated files) or lack of numbers in columns 2 and 3

[dh]

Thank you both, I have edited out the header but still receiving this error. Could it be something to do with the some of the spacing being different?

I am using R to format this using code below so it should uniform, write.table(miR, file="regions.bed", quote=F, sep="\t", row.names=F, col.names=T)

@Pierre Lindenbaum, may I ask what code this is, is this UNIX?

[cpad0112]

Are you using windows? dh