[Genome] Error in liftOver program

[Pauline Fujita]

Hello Peru,

The liftOver program is expecting every line of the BED formatted data 
to be similar to the following:

        chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512

Note that only the first 3 fields are required for liftOver. If you have 
a row in your input that is something other than genomic coordinates - 
for example the track settings line for an annotation track:

        track name=pairedReads description="Clone Paired Reads" useScore=1
        chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512

It will give you an error similar to the one you are getting:

        "Expecting number field 2 line 1 of 
../trash/hglft_genome_468c_49de80.user, got name=pairedReads"

This is because it doesn't like the "name=pairedReads" input. It is 
expecting the first column to be a chromosome name, and the second and 
third columns to be start and end positions. If you want to include 
lines that are not of this format in your input, you can "comment" them 
out by preceding them with a # sign:

        #track name=pairedReads description="Clone Paired Reads" useScore=1
        chr22 1000 5000 cloneA 960 + 1000 5000 0 2 567,488, 0,3512

This should cause liftOver to ignore the first line and run smoothly. 
(Note that the commented lines will not appear in the liftOver results.)

Hopefully this information was helpful and answers your question. If you 
have further questions or require clarification feel free to contact the 
mailing list at genome at soe.ucsc.edu.

Regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

Perumal, Narayanan B wrote:
> Hello,
>
> I got the following error when I was trying to liftover a bed file from mm7 (August 2005) to mm8 (Feb. 2006). Any ideas to solve the problem?
>
> Expecting number field 2 line 1 of ../trash/hglft_genome_147e_472cf0.user, got name="IL12::1
>
> ~Peru
>
> Narayanan Perumal, PhD MSIS
> Assistant Professor
> School of Informatics
> Indiana University - Purdue University Indianapolis
> 719 Indiana Avenue Suite 311
> Indianapolis, IN 46202
> nperumal at iupui.edu
> 317-278-4147
> Web Course: http://www.swbic.org/education/comp-bio/test.htm
>
> ~Peru
>
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