Liftover Error: Expecting At Least 12 Words Line 1

Question

[Aishwarya Kulkarni]

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?

Answer 1

[Pierre Lindenbaum]

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

Answer 2

[Aishwarya Kulkarni]

yes got it thanks!