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FYI, BLAT worked well. I created a series of databases, each containing 7.5 million reads.
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Originally posted by GenoMax View PostBlat should work for this too: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3
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Using Bioconductor
You can simply do it in R.
1. Install the Biostrings package
source("http://bioconductor.org/biocLite.R")
biocLite("Biostrings")
2. Load the Biostrings package
library(Biostrings)
3. Use the matchPattern function. To get a detailed help page for it, type :
?matchPattern
You'll see it has all of the options that you need for your example.
matchPattern(pattern, subject, max.mismatch=0, min.mismatch=0, with.indels=FALSE, fixed=TRUE, algorithm="auto")
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align short query against 300M Illumina reads
Hi,
I have 8 short (~60nt) query sequences which I want to align to roughly 300M Illumina reads (100bp). Criteria are:
- Allow a few mismatches (< 8)
- Gaps are not allowed.
- Alignment should span the entire query.
- Report all matches, NOT just the best one.
Do any programs exists that can accomplish this task? I was thinking BWA, or other next-gen read mappers, but these usually work with whole genomes as their database and reads as the query. The case I have here is somewhat different and may not work with these programs.
Any ideas?
Thanks in advance for the help.Last edited by hohllp; 11-17-2011, 01:49 PM.Tags: None
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