liftOver from hg19 to b38

[Emma Lord]

Hi,

 

I am trying to use the UCSC liftOver to liftover a bed file from hg19 to hg38. I tried using the online tool but it appears that my bed file is too big. When I use command line I get the “invalid unsigned integer: "name="Affymetrix"

error.

 

I am trying to liftover the Affymetrix SNP 6.0 BED file from hg19 to hg38  (http://www.affymetrix.com/Auth/analysis/downloads/lf/genotyping/GenomeWideSNP_6/GenomeWideSNP_6.hg19.bed.zip)

I am using the hg19ToHg38.over.chain.gz to do this.

 

Please could you let me know where I might be going wrong? I’m quite new to all of this, so would appreciate if you can help simplify things, but I believe it might be that the bed file is incorrectly formatted?

 

Many thanks,

Emma Lord

 

[Christopher Lee]

Hi Emma,

Thank you for your question about lifting over a file from hg19 to
hg38. The problem with your file is that the first line contains a
"track line":
https://genome.ucsc.edu/goldenpath/help/customTrack.html#TRACK

Track lines are used to specify certain characteristics when you load
the file as a custom track in the Genome Browser. If you remove or
comment out the track line with a '#' then your file should lift
correctly.

Please let us know if you have any further questions!

Thank you again for your inquiry and using the UCSC Genome Browser. If
you have any further questions, please reply to gen...@soe.ucsc.edu.
All messages sent to that address are archived on a
publicly-accessible forum. If your question includes sensitive data,
you may send it instead to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute

> --
>
> ---
> You received this message because you are subscribed to the Google Groups
> "UCSC Genome Browser Public Support" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to genome+un...@soe.ucsc.edu.
> To post to this group, send email to gen...@soe.ucsc.edu.
> Visit this group at https://groups.google.com/a/soe.ucsc.edu/group/genome/.
> To view this discussion on the web visit
> https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/F494861D-8A94-4BC9-82CE-8B5BC1337B84%40leeds.ac.uk.
> For more options, visit https://groups.google.com/a/soe.ucsc.edu/d/optout.