Hello, One more quick question if you have time - from where did you download the MAF dataset that you are using for the query (the all.maf data)?
Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ 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
