Question: Liftover Error: Expecting At Least 12 Words Line 1
0
gravatar for Aishwarya Kulkarni
5.8 years ago by
United States
Aishwarya Kulkarni60 wrote:

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 • 2.1k views
ADD COMMENTlink modified 5.8 years ago by Istvan Albert ♦♦ 81k • written 5.8 years ago by Aishwarya Kulkarni60
1
gravatar for Pierre Lindenbaum
5.8 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

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

ADD COMMENTlink written 5.8 years ago by Pierre Lindenbaum124k
0
gravatar for Aishwarya Kulkarni
5.8 years ago by
United States
Aishwarya Kulkarni60 wrote:

yes got it thanks!

ADD COMMENTlink written 5.8 years ago by Aishwarya Kulkarni60
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