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
