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Old 05-05-2011, 05:32 PM   #1
sweet_dna_girl
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Default raw sequence short read data

Hi,

Does anyone know where I can find raw short read sequence data? By raw, I mean unfiltered, so that the low quality reads from the machines are included in the data set. I heard that in the 1000 genomes database, the data is filtered by quality.

Thanks!!!
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Old 05-06-2011, 01:01 AM   #2
gaffa
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Well, NCBI's short read archive is generally the place to be: http://www.ncbi.nlm.nih.gov/sra This is a central depository for data from short read experiments.
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Old 05-06-2011, 02:45 AM   #3
ulz_peter
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Just in case you didn't know: NCBI will stop the SRA quite soon:
The following appears on the link you've posted:

Sequence Read Archive (SRA) and Trace Archive repositories have been discontinued

Due to budget constraints, NCBI will be discontinuing its Sequence Read Archive (SRA) and Trace Archive repositories for high-throughput sequence data. Closure of the databases will occur in phases. SRA and Trace will stop accepting some types of submissions in the coming weeks, and all submissions within the next 12 months. Over the next several months, NCBI will be working with staff from NIH Institutes that fund large-scale sequencing efforts to develop an approach for future access to and storage of the existing data. NCBI will continue to support and develop information resources for biological data derived from next-generation sequencing such as genotypes, common variations, rare variations, sequence assemblies and gene expression data. We therefore encourage the research community to continue submissions of these data to the applicable databases, including:

1. RNA-Seq and epigenomic data to GEO
2. Variants, genotypes, phased haplotypes, and polymorphisms to dbVar, dbGaP and dbSNP
3. Genomic assemblies to GenBank/WGS
4. Transcript assemblies to GenBank/TSA
5. 16S ribosomal RNA and other targeted locus survey assemblies to GenBank

NCBI expects new applications will continue to emerge for next generation technology. We are excited to work with the community to develop strategies for archiving other summary experimental measures that are informative, efficient, and valuable to the biomedical research community.

For further information about submissions, contact NCBI's Help Desk.

Best regards
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Old 05-06-2011, 10:10 AM   #4
sweet_dna_girl
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ok thanks for your help! However, how do I know whether the reads in the NCBI archive are filtered or unfiltered?
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Old 02-15-2012, 11:42 PM   #5
Apexy
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Hi sweet_dna_girl,

Did you ever finf an answer to your last question? I think the sequences are unfiltered at least for the data set which I downloaded. I plotted Q-score and found some to be extremely poor. However what I have not been able to figure out is information about that adapters that were used. This could help in cleaning out the adapter sequences. Does any one know where the information associated with the adapter for each run of the SRA data is kept?

Regards,

Mbandi
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