Hi, I found the solution simply by removing the -errorHelp and (as you said) adding -minMatch=0.1
Best, Avi --- On Wed, 5/27/09, Fungazid <[email protected]> wrote: > From: Fungazid <[email protected]> > Subject: Re: [Genome] liftover parametrs > To: "Jennifer Jackson" <[email protected]> > Cc: [email protected] > Date: Wednesday, May 27, 2009, 2:03 PM > > Jennifer hi, > > Thank you for the rapid answer. I will describe the problem > I have, and maybe you can see what is wrong: > > > 1) I created a bed file called test.bed which contains the > following text: > > chr1 3585316 3777472 pos1 > chr2 6585316 6585416 pos2 > chr3 6585316 6585416 pos3 > chr4 6585316 6585416 pos4 > chr5 6585316 6585416 pos5 > > 2) I placed test.bed in the directory where > mm9ToRn4.over.chain is located, CD to this directory, and > started liftOver: > > liftOver ./test.bed ./mm9ToRn4.over.chain ./test2.bed > ./unMapped -errorHelp -minMatch=0.95 > > > 3) This is the message I get: > > Deleted in new: > None of sequence intersects with any > alignment chain for the region > Partially deleted in new: > Sequence intersects with part of a single > alignment chain in the region > Split in new: > Sequence partially intersects multiple chains > in the region > Duplicated in new: > Sequence completely intersects multiple > chains in the region > Boundary problem: > Missing start or end base in an exon > > > > > So: > I do not get any output. > I assume test2.bed and unMapped are the output files, but > they were not created by liftOver (should I create them > first?). In addition what is "Missing start or end base in > an exon" (I used a genomic data, not genes) > > > It should be noted that if I use the same bed file as an > input for the online lifOver (old genome mouse, new genome > human), I get some results: > > conversions: > chr8 56090155 > 56244617 pos1 > chr10 11299218 > 11299320 pos2 > chr7 88976276 > 88976377 pos5 > > failures: > #Deleted in new > chr3 6585316 > 6585416 pos3 > #Deleted in new > chr4 6585316 > 6585416 pos4 > > > > > > > > > > --- On Wed, 5/27/09, Jennifer Jackson <[email protected]> > wrote: > > > From: Jennifer Jackson <[email protected]> > > Subject: Re: [Genome] liftover parametrs > > To: "Fungazid" <[email protected]> > > Cc: [email protected] > > Date: Wednesday, May 27, 2009, 1:04 AM > > Hello Avi, > > > > If you type in the command at the prompt, a list of > options > > will appear along with usage. The over.chain files are > in > > Downloads, ftp directory > > goldenPath/<from_species>/liftOver/. > > > > For default genomic examples, there are two classes: > same > > species lifts and cross-species lifts. Both can be > seen in > > the web version [UCSC Browser home page -> > Utilities > > -> Batch Coordinate Conversion (liftOver)] > > http://genome.ucsc.edu/cgi-bin/hgLiftOver > > > > The most basic option for genomic would be to set > -minmatch > > = 0.95 for same-species and = 0.1 for cross-species > and > > leave the rest as default. > > > > For any failures, you can examine the reasons and > play > > around with the parameters, such as setting multiple = > Y. > > But beware that this can produce significant output > if > > minmatch is low and chain and hit size are set >= > 0. It > > will probably take a few attempts to tune these in > various > > combinations so that the output is useful for your > > particular needs. > > > > The other options come into play for gene, transcripts > and > > other annotation types that are lifted. Again, the > program > > runs pretty fast even on large datasets, so a cyclic > > test-and-analyze approach is probably the best way to > find > > your own best parameters to create useful lifted > data. > > > > FAQ in case you have not seen it: > > http://genome.ucsc.edu/FAQ/FAQdownloads#download28 > > > > Good luck and please write back if you need more > technical > > help, > > Jennifer Jackson > > UCSC Genome Bioinformatics Group > > > > Fungazid wrote: > > > hello genome browser staff, > > > > > > I would like to map species A genomic coordinates > to > > species B genomic coordinates (e.g. mouse -> > human). To > > my knowledge liftover can do it (I also tried to > workaround > > by blating the query region with gfserver/gfclient, > but this > > is too slow for large tables). I have Liftover > installed on > > Linux, but I didn't find any documentation about > input > > parameters and examples. Maybe you can help, or direct > me to > > a proper documentation. > > > > > > Thanks, (also you for your previous help) > > > Avi > > > > > > > > > > > _______________________________________________ > > > Genome maillist - [email protected] > > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > > > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
