Galt, It has worked with the same blat. I never realized that this could be the database. I had used data from separate chromosomes files of mm9 assembly and then concatenated them. I'm not sure what's missing but as long as it works I'm fine with mm9.2bit.
Thanks a lot for helping with this. perdeep -----Original Message----- From: Galt Barber [mailto:[EMAIL PROTECTED] Sent: Tuesday, November 25, 2008 12:29 PM To: Mehta, Perdeep Cc: 'Galt Barber' Subject: RE: [Genome] Blat question I am using the latest source code. It might not be the official release yet. You can download the entire kent source tree which would contain blat among other thigns. On the other hand, the difference between your version and mine might not matter. I am trying this: http://www.soe.ucsc.edu/~kent/src/blatSrc34.zip with this: http://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/mm9.2bit Looks like I still found the 6-B alignment an chr7: 30 1 0 0 0 0 0 0 + 6-B 66 35 66 chr7 152524553 144313185 144313216 1 31, 35, 144313185, [hgwdev:mehta> grep chr7 out.ps | grep 6-B | vlist -tab -format=$HOME/psl.fmt matches - Number of bases that match that aren't repeats : 30 misMatches - Number of bases that don't match : 1 repMatches - Number of bases that match but are part of repeats : 0 nCount - Number of 'N' bases : 0 qNumInsert - Number of inserts in query : 0 qBaseInsert - Number of bases inserted in query : 0 tNumInsert - Number of inserts in target : 0 tBaseInsert - Number of bases inserted in target : 0 strand - '+' or '-' for query strand. For translated alignments, second '+'or '-' is for genomic strand : + qName - Query sequence name : 6-B qSize - Query sequence size : 66 qStart - Alignment start position in query : 35 qEnd - Alignment end position in query : 66 tName - Target sequence name : chr7 tSize - Target sequence size : 152524553 tStart - Alignment start position in target : 144313185 tEnd - Alignment end position in target : 144313216 blockCount - Number of blocks in the alignment (a block contains no gaps) : 1 blockSizes - Comma-separated list of sizes of each block : 31, qStarts - Comma-separated list of starting positions of each block in query : 35, tStarts - Comma-separated list of starting positions : 144313185, ---------------------------------------- _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
