Dna Sequencers 150 Bps Output File

Question

[Arpssss]

I am doing some experiment using BowTie which is a short read aligner that aligns short DNA sequences (reads) to the human genome. Now, I want, to experiment with it on 150 bps reads. So, I want DNA sequencers 150 bps output file. For example, output of this (Genome Analyzer IIx). Can anybody please help me, where can I find it ? Or is there any BioInfo community who can help me about this ?

Answer 1

[Zev.Kronenberg]

Are you just looking for raw sequencing reads? If so: Short Read Archive should have what you want.

SRA

The main page states:

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, Helicos Heliscope®, Complete Genomics®, and Pacific Biosciences SMRT®.

One example experiment:

data

[Arpssss]

No. I want format like http://en.wikipedia.org/wiki/FASTQ_format (see Encoding section, at the last of the page) but for 150 bps.

[Zev.Kronenberg]

The Short Read Archive contains FASTQ data. They have a conversion script to dump SRA to FASTQ.

[Arpssss]

Thanks a lot. But, I really don't find any folder saying that they contains, 150 bps length Short Read.

[Zev.Kronenberg]

see changes to main post above.

Answer 2

[Hamish]

Well you could look in the European Nucleotide Archive (ENA). From a quick query ENA contains a number of sequencing runs produced using the Genome Analyzer IIx ("instrument_model=Illumina Genome Analyzer IIx"), so they would be a place to start.

The ENA provide Web Services (see http://www.ebi.ac.uk/ena/about/browser), and the experiment meta-data is available so you can automate your search for appropriate experiments, and fetch the referenced FASTAQ data from the FTP site.