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asntech / intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets
http://intervene.rtfd.io/
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Bedtools intersect error #19

Closed jaqx008 closed 5 years ago

jaqx008 commented 5 years ago

Hello GitHub Users, I am running a shell script and during the run I get this error although the script goes on to finish but its not generating my intersect bed. the portion of the script the error is coming from is 

bedtools intersect -wa -a TE.bed -b "$i".allMap.bed | \
        awk '{print $1":"$2"-"$3}' | sort | uniq -c | awk '$1 > 50' | \
        awk '{print $2"\t"$1}' > "$i"TEtargets.txt
        bedtools intersect -wa -a mRNA.bed -b "$i".allMap.bed | \
        awk '{print $1":"$2"-"$3}' | sort | uniq -c | awk '$1 > 50' | \
        awk '{print $2"\t"$1}' > "$i"mRNAtargets.txt

The Error is below

ERROR: illegal character ' ' found in integer conversion of string "7 556442". Exiting...

asntech commented 5 years ago

Hi, You need to file this issue here: https://github.com/arq5x/bedtools/issues

Thanks!