Hello,
I have a task in hand to perform sequence alignment using blat. Unfortunately, I have approximately 500+ individual sequences and the web-blat on ucsc's web-portal would not cater more than 25 at a time. For that reason, I went ahead and installed blat on my local server. Ran the sequence alignment executable 'blat' against my Hg sequences and everything ran to completion using a command-line based run. But when I compared my commad-line results with the web-based results from UCSC for the same sequence, there seem to be some difference. I have not set any flags or configured my command-line version of the blat and it commands of execution looks like: blat -out=blast9 hg18.2bit test_seq.txt test_seq_blas9.out I tried the FAQ recommendation on the UCSC's blat web-space for the recommended flags to use to reproduce web-based blat results and get the following error: blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 -out=blast9 hg18.2bit test_seq.txt test_seq_blas9.out needHugeMen: Out of huge memory - request size 2106194880 bytes I know for the fact I have loads of memory on my workstation. Is there a big algorithmic difference in the way the web-blat and commad-line default blat operate? For reproducible research purpose I would like for my command-line blat to report the same results as the web-based blat (on ucsc's web portal) Any recommendations, thoughts, comments will be appreciated. Many Thanks, Vinodh _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
