Question: LiftOver no id column
0
gravatar for melfaramawi
2.0 years ago by
melfaramawi0 wrote:

I have a question related to LiftOver. LiftOver output does not allow any id columns in the output: It deletes them from the input. I have tried several tricks but no luck at. e.g I have prepared bed files that have the following structures: track name=coords description="Chromosome coordinates list" chr22 14577021 14577024 ak1 chr22 15333560 15333563 ak2

track name=coords description="Chromosome coordinates list" column-4 chr22_1 14577021 14577024 chr22_2 15333560 15333563

track name=LitOver description="Chromosome coordinates list"
1.chr22 14577021 14577024 2.chr22 15333560 15333563

Always I get the output shown below:

chr22:16197021-16197024

chr22:16959006-16959008

I want the output to have an id column I am adding in the bed file (4th column) so that I can link the output to the original Map file. Any suggestions, please Thanks.

ucsc format liftover galaxy output • 609 views
ADD COMMENTlink modified 2.0 years ago by Jennifer Hillman Jackson25k • written 2.0 years ago by melfaramawi0
0
gravatar for Jennifer Hillman Jackson
2.0 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The tool does not report the name ("id") field in the output. This is the default output format of the liftOver command utility from UCSC. The tool is wrapped in Galaxy without any modifications.

Reference (be sure to see the links at the bottom of the form): http://genome.ucsc.edu/cgi-bin/hgLiftOver.

If you need to know the coordinates for a specific region (single input line), just input that. I do not know of a way to include a tag, name or otherwise, to track input line to output line - and I worked at UCSC for many years prior to Galaxy. However, if you wish to ask the UCSC team if this is somehow possible now, searching their FAQ plus prior Q&A or contacting them directly is suggested: https://genome.ucsc.edu/contacts.html

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.0 years ago by Jennifer Hillman Jackson25k

Thanks Jennifer for your comment

ADD REPLYlink written 2.0 years ago by melfaramawi0
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