Questions tagged [blat]

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2 votes
2 answers
82 views

How to get the genomic sequences from a blat result?

Assume we have a query.fa file that contains sequences and we run: ...
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  • 1,347
1 vote
0 answers
35 views

setting BLAT alignment parameters to give long matches

I'm using BLAT to align DNA sequences between similar species, and having trouble setting the parameters to return only significant matches along the 50bp query lengths. Using ...
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  • 305
4 votes
1 answer
280 views

Can blat use more than one core/CPU to speed up the alignment?

I am using BLAT to align two versions of the genome of C. elegans. I can see in the Activity Monitor of my Mac Book Pro High Sierra that blat is using 100% of a CPU....
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4 votes
1 answer
147 views

Using large databases with BLAT

I'm a computer scientist working with biologists at a small school that doesn't have dedicated bioinformatics staff. I apologize if I use incorrect terminology since I have limited bioinformatics ...
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  • 41
4 votes
1 answer
566 views

Using BLAT command line tool to blat split sequences

I have the nucleotide sequence: AATTGAGGCACATTTTTTTTTAGACAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGTGGTGTGATCATAGCTCACTGCAGCCTCGACCTCCTGGGCTCAACAAAGCACACAGTGGGCGGATCCCCACCAG When I blat this on UCSC Genome ...
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  • 249
7 votes
2 answers
535 views

Understanding the significance of BLAT score calculations for read fragment alignment

I'm attempting to reconstruct the read fragments that form a hit to a target, excluding/skipping gaps. BLAST's outfmt 6, and alternatives such as Diamond's ...
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