Getting Bedtools Error

Question

[raghus606]

Hello Everyone,

I am trying to run bedtools intersect to find which genes are present in each of the locations I have in a bed file.

No matter what I do I get an error like:

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

I was trying to intersect with a bed file from table browser but even if I try to intersect this file with itself I get the above error.

I am using the command:

bedtools intersect -a temp.bed -b temp.bed

There are no white spaces in b/w and it is tab delimited properly.

Anyone knows what is going on?

Thank You

My file is like this (temp.bed):

chr1     213296337     213296346
chr2     25466989     25466991
chr2     198267293     198267295
chr4     106155869     106155898
chr4     106155869     106155898
chr4     106156040     106156077
chr4     106156604     106156689
chr4     106156604     106156614
chr4     130626272     130626278
chr7     50467731     50467743
chr7     101845055     101845144
chr7     101870826     101870827
chr7     101891788     101891789
chr7     148512684     148512708
chr8     32273913     32273915
chr8     117862888     117862895
chr8     117868550     117868555
chr8     117868561     117868565
chr8     117868562     117868565
chr8     117868562     117868565
chr9     21968208     21968246
chr9     139391118     139391119
chr11     118352462     118352463
chr12     11803035     11803036
chr17     7579292     7579322
chr18     62519039     62519105
chr19     32655439     32655531
chr19     45303778     45303780
chr19     45303921     45303922
chr20     55611177     55611287
chr21     36259110     36259114
chr21     36421116     36421146
chrX     15808821     15808822
chrX     15827406     15827407
chrX     15827404     15827408
chrX     39923803     39923812
chrX     39930429     39930484
chrX     39930433     39930446
chrX     39930433     39930447
chrX     39930575     39930580
chrX     39931816     39931845
chrX     44918176     44918249
chrX     44928977     44928978
chrX     123184866     123184968
chrX     123184867     123184870
chrX     123184993     123184995
chrX     123185031     123185034
chrX     123195741     123195782
chrX     123199698     123199768
chrX     123228015     123228031
chrX     129147408     129147413
chrX     129162905     129162911
chrX     129162905     129162911
chrX     129162905     129162912
chrX     129162907     129162911
chrX     129162905     129162911
chrX     129162911     129162912
chrX     129162911     129162916
chrX     129162912     129162917
chrX     129162912     129162917
chrX     129162912     129162917
chrX     129162912     129162921
chrX     129162912     129162921
chrX     129162969     129162971
chrX     129162977     129162978
chrMT     5431     5440
chrGL000241.1     2336     2346

[raghus606]

Thank You that seemed to do the trick, there was indeed a space.

I was doing print chr,"\t",start,"\t",stop while generating it in python, changing it to print chr+"\t"+start+"\t"+stop fixed it.

Answer 1

[Alex Reynolds]

If you want to try validating your input, you could use BEDOPS [bedops --ec], e.g.,:

$ bedops --ec --everything test.bed > /dev/null

This may help direct you to any formatting or ordering issues.

[Alex Reynolds]

You're welcome!