Thanks for your helping, I guess I figured it out. It's cause by the overlapping regions in my bed file.
In my previous bed file, the regions were defined as : *chr13 23449265 23449271 seq1 chr13 23449268 23449275 seq2* So the output for second region is interfered. Once I delete the first line (region) in bed file, it turns to correct output. BTW, the maf file was converted from axt file by uing axtToMaf. The axt files were download from UCSC pairwise alignments. Bests On Tue, Mar 9, 2010 at 8:14 AM, Jennifer Jackson <[email protected]> wrote: > 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
