I am thinking the current supplied (pre-formatted) blastn humangenomic database from NCBI contains many many duplications of the same sequences. Is this correct? I think I only need the current (GRCh37.p5) release of the human genome but blastn typically gives about a dozen identical matches for each (short, 36 nt) query. This must be a common problem. Has anyone built a version of the database which contains _only GRCh37 sequences?
A related problem is that bowtie uses its own database format and the version I have is slightly older than NCBI's current reference sequence. At least that is my current thought about why output from bowtie and blastn do not tie up. Perhaps this is also a common problem? Has anyone succeeded in building the blastn and bowtie databases from a common source? Perhaps this is already available but I have missed it?
Any help or suggestions would be most welcome
Bill
ps: the font on this www page is too small:-(