Liftover Error: Expecting At Least 12 Words Line 1
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8.5 years ago

Hi I am running the ucsc liftover(hg18 to hg 19) for a bed file(the bed file has no header) My command is

./liftOver hg18ToHg19.over.chain.gz ABCD.bed ABCD_hg19_processed.bed ABCD_unlifted.bed

However it gives following error:

Reading liftover chains
Expecting at least 12 words line 1 of ABCD.bed

Is this a common error? If so what is the reason for the same?

liftover • 3.3k views
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1
Entering edit mode
8.5 years ago

I guess you confused the chain files ( http://hgdownload.cse.ucsc.edu/goldenpath/hg19/liftOver/ ) and the input file (Bed).

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Entering edit mode
8.5 years ago

yes got it thanks!

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