align short query against 300M Illumina reads

[hohllp]

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.

[Dario1984]

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")

[hohllp]

Thanks. I'll give it a go.

[GenoMax]

Blat should work for this too: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3

[hohllp]

Blat should work for this too: http://genome.ucsc.edu/FAQ/FAQblat.html#blat3

I am currently trying BLAT. Cannot build a database that large so splitting the 300M reads into subsets.

[hohllp]

FYI, BLAT worked well. I created a series of databases, each containing 7.5 million reads.