running Grch37 to grch38 liftover tool locally

[lre1234]

Hi all,

I am trying to run the UCSC ligtover tool on my local machine (linux version), but am running into some difficulties.

my input file is a standard bed:

chr1    17369   17391   miR-6859-3p

and to run the tool I am doing this (as specified by their usage):

./liftOver -errorHelp my_hg19.bed hg38ToHg19.over.chain my_new.bed unMapped

I keep getting this error:

Deleted in new:
    Sequence intersects no chains
Partially deleted in new:
    Sequence insufficiently intersects one chain
Split in new:
    Sequence insufficiently intersects multiple chains
Duplicated in new:
    Sequence sufficiently intersects multiple chains
Boundary problem:
    Missing start or end base in an exon

Yet if I run this directly on the USCS website, it runs just fine.

I must be doing something wrong, but can't quite figure it out.....

[WhatsOEver]

were do they specify this usage?

you simply need to remove "-errorHelp"
This just prints the help for error messages (which is your ouptput), everything after it is ignored

[GenoMax]

What direction are you trying to go with liftover? Title of your post says Grch37 to Grch38 but you seem to be using the chain file for going the other direction.

[lre1234]

Yes, I am trying to go from Grch37 to Grch38. I can't seem to find the chain file to go the other (and didn't realize the I had the wrong one).

The specified usage is:

liftOver - Move annotations from one assembly to another
usage:
   liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and
maybe eventually others with the appropriate flags below.
The map.chain file has the old genome as the target and the new genome
as the query.

***********************************************************************
WARNING: liftOver was only designed to work between different
         assemblies of the same organism. It may not do what you want
         if you are lifting between different organisms. If there has
         been a rearrangement in one of the species, the size of the
         region being mapped may change dramatically after mapping.
***********************************************************************

options:
   -minMatch=0.N Minimum ratio of bases that must remap. Default 0.95
   -gff  File is in gff/gtf format.  Note that the gff lines are converted
         separately.  It would be good to have a separate check after this
         that the lines that make up a gene model still make a plausible gene
         after liftOver
   -genePred - File is in genePred format
   -sample - File is in sample format
   -bedPlus=N - File is bed N+ format
   -positions - File is in browser "position" format
   -hasBin - File has bin value (used only with -bedPlus)
   -tab - Separate by tabs rather than space (used only with -bedPlus)
   -pslT - File is in psl format, map target side only
   -ends=N - Lift the first and last N bases of each record and combine the
             result. This is useful for lifting large regions like BAC end pairs.
   -minBlocks=0.N Minimum ratio of alignment blocks or exons that must map
                  (default 1.00)
   -fudgeThick    (bed 12 or 12+ only) If thickStart/thickEnd is not mapped,
                  use the closest mapped base.  Recommended if using 
                  -minBlocks.
   -multiple               Allow multiple output regions
   -minChainT, -minChainQ  Minimum chain size in target/query, when mapping
                           to multiple output regions (default 0, 0)
   -minSizeT               deprecated synonym for -minChainT (ENCODE compat.)
   -minSizeQ               Min matching region size in query with -multiple.
   -chainTable             Used with -multiple, format is db.tablename,
                               to extend chains from net (preserves dups)
   -errorHelp              Explain error messages

Even removing the 'errorHelp' just gives back this usage help.

[GenoMax]

Yes, I am trying to go from Grch37 to Grch38. I can't seem to find the chain file to go the other (and didn't realize the I had the wrong one).

Here is the chain file for hg19toGrch38: http://hgdownload.soe.ucsc.edu/golde....over.chain.gz

[lre1234]

Thank you. That works!!