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
