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-   -   total RNA/transcriptome of E.coli or S.cerevisiae (http://seqanswers.com/forums/showthread.php?t=30906)

SquirrelSeq 06-06-2013 07:14 AM

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

sudhirvarma 06-06-2013 08:30 AM

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

SquirrelSeq 06-07-2013 06:45 AM

Thank you for your help, that was highly useful!

SquirrelSeq 06-12-2013 05:02 AM

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)

TonyBrooks 06-12-2013 05:05 AM

Quote:

Originally Posted by SquirrelSeq (Post 107431)
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?

SquirrelSeq 06-12-2013 05:20 AM

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

peter pfand 01-21-2015 02:24 AM

Is there anything similar but for microarray data?

Thanks


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