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Old 06-06-2013, 07:14 AM   #1
SquirrelSeq
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Default total RNA/transcriptome of E.coli or S.cerevisiae

Hello everybody,

I'm looking for a repository/archive/database, where I can download FASTQ files of NGS Deep Sequencing runs of E.coli and S.cerevisiae.

Can anybody tell me, where I can find such data publicly available?

Best regards,
SquirrelSeq
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Old 06-06-2013, 08:30 AM   #2
sudhirvarma
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Default SRA is the source

Hi SquirrelSeq
The NCBI Short Read Archive has several E. coli and S. cervisiae datasets, e.g.

E. coli

S. cervisiae

They are in the "sra" format (not FASTQ) which makes the file size smaller to download. SRA has a tool that will easily convert the sra format to fastq. Use the install instructions from here. What you need is the "fastq-dump" tool

Sudhir
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Old 06-07-2013, 06:45 AM   #3
SquirrelSeq
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Thank you for your help, that was highly useful!
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Old 06-12-2013, 05:02 AM   #4
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I downloaded several promising libraries.

Some of them are documented not very detailedly. Before mapping, I normally trim adapters and primers. Are these already trimmed in the public data usually? Otherwise, how should people be able to map the sequences?
(e.g. in 36bp short reads)
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Old 06-12-2013, 05:05 AM   #5
TonyBrooks
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Quote:
Originally Posted by SquirrelSeq View Post
I downloaded several promising libraries.

Some of them are documented not very detailedly. Before mapping, I normally trim adapters and primers. Are these already trimmed in the public data usually? Otherwise, how should people be able to map the sequences?
(e.g. in 36bp short reads)
Why not run the fastq through fastqc to check whether they even need trimming?
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Old 06-12-2013, 05:20 AM   #6
SquirrelSeq
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That is an idea. But as far as I know, I could only see enriched sequences. Is this really enough, to identify primers/adapters? Also other sequences could be enriched, especially in specific samples, such as ribosomal RNA
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Old 01-21-2015, 02:24 AM   #7
peter pfand
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Is there anything similar but for microarray data?

Thanks
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