Hi, Kwame! You probably are a little low on RAM for doing a whole-genome assembly. I would break it into two runs of 10 and 10 chromosomes. e.g. blat [...] outputName.run1 blat [...] outputName.run2
Simply concatentate the two output psl files together. Then use pslReps or pslCDnaFilter to do further filtering as needed. If you want to create a little more stability across the runs in terms of what over-used tiles are masked, you can make a .ooc file and then use it as an option in your blat runs. http://genome.ucsc.edu/FAQ/FAQblat.html#blat6 Here is the command we used for susScr2 (Sscrofa9.2) blat susScr2.2bit /dev/null /dev/null -tileSize=11 -makeOoc=susScr2.11.ooc -repMatch=750 Galt Barber UCSC Genome Browser Staff 2/3/2011 9:04 AM, [email protected]: > Hello, > I am very new to BLAT,Python,Linux. > I want to find out where 19940 genes of Sscrofa9 match on the new build > 10(Sscrofa 10) by doing blat on linux. So I have one file (query) which > contains all the 19940 gene sequences in fasta format. There are 20 target > files containing each containing a chromosome sequence of Sscrofa 10 also in > fasta format. > > I want to blat the query file against each of the 20 target files. > This is the command I am using in python script on linux: > command="blat/blat -minIdentity=95 -minScore=60 -t=dna -q=dna -mask=lower > -fastMap -repMatch=1000000 "+target file+" "+query file+" "+outputName; > > This initiates something but never finishes. However when I reduce the query > file sequences to 10 sequences, it works perfectly. > > Could you please advice me on how to change the options and any other thing > that I have to do so I can run blat with all the 19940 gene sequences at a > go. I hope to hear from you soon. > The capacity of my computer is 2.66GHz, 3.25GB of RAM. > Kwame > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
