Entering edit mode
7.4 years ago
mirza
▴
180
Hi,
I am trying to map my illumina PE reads on two Rhizoctonia solani genome,AG1-IA and AG1-IB. I have downloaded the fasta files for AG1-IA genome from RSIADB (http://genedenovoweb.ticp.net:81/rsia/index.php?m=download&f=index) and AG1-IB scaffolds from JGI portal (http://genome.jgi.doe.gov/pages/dynamicOrganismDownload.jsf?organism=Rhiso1). I am using tophat2 and built the index files using the bowtie2-build command as given in the manual. AG1-IA genome is working fine and I am getting more than 75% aligned reads as expected. But when I am using AG1-IB genome, the reads are not mapping (showing an alignment of <1%) which shouldn't be the case as both are members of the same species. What could be the problem?
