Liftover Error: Expecting At Least 12 Words Line 1

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

• 4,750 views • link

updated 12.5 years ago by Istvan Albert

• written 12.5 years ago by Aishwarya Kulkarni

2 answers

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

• 144 views • link

written 12.5 years ago by Pierre Lindenbaum

yes got it thanks!

• 0 views • link

written 12.5 years ago by Aishwarya Kulkarni

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