Hi I have a question regarding BLAT on command line and BLAT on web browser.
I am getting different results when I run the same query sequence in the following way: 1. Query sequence run in command line BLAT against hg18 2 bit format blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 ~/Projects/Tandem_Repeats/NS_SNP_assoc/BLAT_results_Real_NanostringData/SNP_Genotype/All_Pop_Seperate/Correlation/Correlation_Results_Summary/OTHERS/Human.2bit /home/brahmm01/Projects/BLAT/Query_Sequence.txt Results_blat_hg18.psl 2. Query sequence run in command line BLAT against only chr14 in 2 bit format ( I am considering only chr 14 as the hits on this chromosome are of my prime interest) blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 ~/Projects/Tandem_Repeats/NS_SNP_assoc/BLAT_results_Real_NanostringData/SNP_Genotype/All_Pop_Seperate/Correlation/Correlation_Results_Summary/OTHERS/chr14.2bit /home/brahmm01/Projects/BLAT/Query_Sequence.txt /home/brahmm01/Projects/BLAT/Query_blat_chr14.psl 3. Query sequence run in command line BLAT against only chr14 in 2 bit format with output format as blast output 4. blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 /home/brahmm01/Projects/BLAT/chr14.2bit /home/brahmm01/Projects/BLAT/Query_Sequence.txt out=blast8 /home/brahmm01/Projects/BLAT/Results_blat_chr14.blast.txt 5. Query sequence run on the web browser I am not sure why I am getting different results in terms of the start and end positions of the target region. Manisha Manisha Brahmachary, Department of Genetics and Genomic Sciences Prof. Andrew J. SHARP laboratory Mount Sinai School of Medicine Icahn Medical Institute, Room L14-02 1425 Madison Avenue, Box 1498 NY-10029, NEW-YORK, USA Email:[email protected]
>cg19008523 CTCCCAGGTTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCATGCGCCACCACGCCCAGCTAATTTTGTATTTTTAATAGAGAGAGGGTTTCTCCATGTTGGTCAG
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