Hi Irix, The problem might be with files being overwritten or not written at all (depends if you have noclobber set in your shell or not) in the outDir. These out files are named by the my_regions.bed "name" field. Therefore, only one exist at a time in the same directory.
Try out a test example using the option out.maf instead and see if multiple regions are retrieved. This worked for me and a simple test case. Is this how you run the program (using out.maf, not a directory) when extracting just "a single region in bed file"? It seems as if it would have to be, but please let us know if this is not the case. Please check this and let us know if this solves the problem, Jennifer On 3/7/10 11:24 AM, irix fun wrote: > Hi, > > I am trying to extract several alignments by using "mafsInRegion". > The regions were stored in a bed file. After running a command like: > "*mafsInRegion -outDir my_regions.bed out_dir all.maf " , * > * > * > a alignment is produced for each region, however, some of them are not > complete instead a piece of desired alignment. > > For example: > > The region was specified as following line in bed file: > > *chr13 23449268 23449275 region1* > > And, I got a alignment like: > > *##maf version=1 scoring=blastz* > *a score=0.000000* > *s mm9.chr13 23449272 3 + 120284312 CAC* > *s hg19.chr6 26638647 3 + 171115067 CAC* > * > * > while the correct one should be: > > ##maf version=1 scoring=blastz > a score=0.000000 > s mm9.chr13 23449268 7 + 120284312 AAGGCAC > s hg19.chr6 26638643 7 + 171115067 AAGGCAC > > Finally, it seems that this problem only happened when I tried to extract > multiple regions. It works well for just one region defined in bed file. > > Any suggestions? Thanks a lot. > > Cheer > > > > * > * > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
