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Old 01-05-2009, 12:06 AM   #1
hannat
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Default where can i found raw data generated by solexa

i am going to start ChIP Seq analysis, but i haven't got any data yet, so before that i would like to familiar myself with the raw output of solexa, and practice a little bit, does anyone know where can i found free raw data generated by solexa sequence machine?

many thanks
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Old 01-06-2009, 06:24 AM   #2
chris
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You can try the Short Read Archive at the NCBI http://www.ncbi.nlm.nih.gov/Traces/home/

You can get data in various formats there.

Supposedly, the GEO repository (http://www.ncbi.nlm.nih.gov/projects/geo/) should also have some, but all I can find is processed data. Plus, it's mainly microarray data so it's difficult to find any solexa in there.
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Old 01-06-2009, 12:25 PM   #3
Chipper
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http://www.bcgsc.ca/data/chipseq
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Old 01-06-2009, 10:22 PM   #4
hannat
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Thanks a lot.
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Old 01-12-2009, 06:56 AM   #5
cochrane
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In addition to the NCBI service, you can download submitted SRF files from the EBI's European Read Archive (ENA-reads) from ftp://ftp.era.ebi.ac.uk/. We support both anonymous FTP and non-anonymous Aspera data downloads. Aspera accounts are created upon request.

The directory structure is [volM]/ERANNN/ERANNNNNN/srf; the volN root directory is not visible at the time of writing but will be soon there. The ERANNNNNN is the submission accession number. The XML metadata is available at ftp://ftp.era-xml.ebi.ac.uk/ organized by submission accession numbers as well.

To point you directly to some actual data: you can find SRFs submitted by the Sanger Institute as part of the 1000 Genomes Project for Human HapMap individual NA07000 in submission ERA000024.


ftp://ftp.era.ebi.ac.uk/ERA000/ERA000024/srf


The first eight files are the lanes from a single Illumina machine run.

SAMPLE_NAME FILE_NAME CENTER_NAME STUDY_NAME INSTRUMENT_MODEL LIBRARY_LAYOUT BASE_COUNT READ_COUNT CYCLE_COUNT RUN_ID SUBMISSION_ID
Human HapMap individual NA07000 1004_s_1.srf SC 1000Genomes Project Pilot 1 Solexa 1G Genome Analyzer PAIRED 497344232 6720868 74 ERR001032 ERA000024
Human HapMap individual NA07000 1004_s_2.srf SC 1000Genomes Project Pilot 1 Solexa 1G Genome Analyzer PAIRED 511236474 6908601 74 ERR001033 ERA000024
Human HapMap individual NA07000 1004_s_3.srf SC 1000Genomes Project Pilot 1 Solexa 1G Genome Analyzer PAIRED 509881534 6890291 74 ERR001034 ERA000024
Human HapMap individual NA07000 1004_s_5.srf SC 1000Genomes Project Pilot 1 Solexa 1G Genome Analyzer PAIRED 517990084 6999866 74 ERR001035 ERA000024
Human HapMap individual NA07000 1004_s_6.srf SC 1000Genomes Project Pilot 1 Solexa 1G Genome Analyzer PAIRED 521491690 7047185 74 ERR001036 ERA000024
Human HapMap individual NA07000 1004_s_7.srf SC 1000Genomes Project Pilot 1 Solexa 1G Genome Analyzer PAIRED 513700008 6941892 74 ERR001037 ERA000024
Human HapMap individual NA07000 1004_s_8.srf SC 1000Genomes Project Pilot 1 Solexa 1G Genome Analyzer PAIRED 498362916 6734634 74 ERR001038 ERA000024



Quote:
Originally Posted by hannat View Post
i am going to start ChIP Seq analysis, but i haven't got any data yet, so before that i would like to familiar myself with the raw output of solexa, and practice a little bit, does anyone know where can i found free raw data generated by solexa sequence machine?

many thanks
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