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Bedtools Error: Type checker found wrong number of fields while tokenizing data line.

Hi,

I get an error for having an extra tab but removing the extra tab does not solve the error, has anybody run into this?

cat bed1.txt bed2.txt | sort -k1,1 -k2,2n | mergeBed -i stdin > merged.bed

Error: Type checker found wrong number of fields while tokenizing data line. Perhaps you have extra TAB at the end of your line? Check with "cat -t"

sed 's/\t$//' bed1.txt > bed1.corrected.txt

Doesn't work. I also tried to replace all spaces/tabs and then reformat into a tab-delimited, but I get the same error. 

awk '{$1=$1};1' bed1.txt | sed 's/ /\t/g' > bed1.corrected.txt
bedtools
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updated by Alex Reynolds Alex Reynolds • written by User 7754 User 7754

Perhaps you have extra TAB at the end of your line? Check with "cat -t"

did you try this ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Yes; but shouldn't the sed command get rid of them?

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written by User 7754 User 7754

none of your commands above remove the trailing tabs.

try

sed 's/[\t]*$//' bed1.txt > bed1.corrected.txt
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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre, thank you, I have tried that but I still get the same error after doing that to each bed file: cat bed1.corrected.txt bed2.corrected.txt | sort -k1,1 -k2,2n | mergeBed -i stdin > merged.bed

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written by User 7754 User 7754

1 answer

So long as inputs have at least three columns, the following use of BEDOPS tools should work on inputs with different numbers of columns (or lines with lone tabs at the end):

$ cat bed1.txt bed2.txt | sort-bed - | bedops --merge - > answer.bed

The merged output will only have three columns.

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written by Alex Reynolds Alex Reynolds

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