galt, On Jul 14, 2009, at 12:12 PM, Galt Barber wrote:
> Looking at the source code for gfServer, it seems to ignore the - > mask option for untranslated use. I shoulda dug around in the source... sorry to be a little lazy... > It does appear that you will need to use standalone blat if you want > to use masking options. Many users for untranslated don't even > bother with explicit masking. There is still some "masking" that > occurs by virtue of overused tiles being ignored and thus unable to > initiate a hit. our sequences are heavy with long repetitive elements, so we're just trying to avoid repeat-repeat, high-scoring/match % targets without extra parsing, for simplicity and speed. > It was unclear to me why you were saying that you needed gfServer > instead of standalone blat to run many queries. You can have an > enormous set of queries with standalone blat. For the original series of queries I was running, blat was giving me the out of memory/'segmentation fault' (i believe i was using a 32-bit binary with hg18 and/or mm9 w/ 4 GB free RAM). gfServer appeared to be more friendly - thus the reason I *started* using it in place of blat. Procedurally, it was also a little easier to fire off the queries one-at-a-time because (1) I was piping inputs and outputs around and I was attempting to reduce the memory load, (2) i was parsing the results into a database, and query by query was just simpler to implement, and (3) i was imagining a future scenario where we have different gfServers running on a remote machine(s) with lower RAM clients (running the code) pinging the appropriate server/port for their result. I'll give blat a shot with a large set of inputs (we have groups of ~ 20,000, 200-400 mers) and see if that fits into the workflow well/ increases speed, which I imagine it will. Otherwise, standalone blat is working perfectly (with a smaller 2bit file) for what we're doing, so it's looking like i'll stick with it ; ). thanks again for your fast response and have a good one! cheers, -b < * ) (_ \\ _ || _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
