Question: RNAseq raw data for expression analysis
0
gravatar for shuksi1984
2.3 years ago by
shuksi198460
shuksi198460 wrote:

Where can I get RNAseq raw data (paired end fastq format) for expression analysis?

rna-seq • 1.6k views
ADD COMMENTlink modified 2.3 years ago by grant.hovhannisyan2.0k • written 2.3 years ago by shuksi198460

You will get something relevant here I guess : Where Can I Find Fastq Data (Ngs Raw Data) And Published Results?

ADD REPLYlink written 2.3 years ago by Bastien Hervé4.7k
1
gravatar for grant.hovhannisyan
2.3 years ago by
grant.hovhannisyan2.0k wrote:

Dominating resources are Sequence Read Archive (SRA) database and European Nucleotide Archive (ENA). From ENA you can download fastq files directly, from SRA you have to download .sra format and then convert it to fastq using fastq-dump for example. I personally prefer SRA because I like its search and query building engine.

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by grant.hovhannisyan2.0k

I am trying to download the data from the following link: https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?exp=SRX317694&cmd=search&m=downloads&s=seq sra_data.fastq.gz >3.0GB as it is downloading since last 4hrs. I suppose I am downloading the correct file.

ADD REPLYlink written 2.3 years ago by shuksi198460

Yes it seems to be the correct file. Note that for downloading and converting files from SRA you better use sratoolkit, which is a command line-based set of tools to work with SRA.

ADD REPLYlink written 2.3 years ago by grant.hovhannisyan2.0k

After downloading and unzipping I got 17G sra_data.fastq file. But I need paired end data, as per the link it is paired end, but after extraction there is only one fastq file. I am confused at this point of time.

ADD REPLYlink written 2.3 years ago by shuksi198460

How exactly have you download the data? For me fastq-dump --split-3 SRR925687 worked perfectly well downloading paired end reads (each file is 8.4 Gb)

ADD REPLYlink written 2.3 years ago by grant.hovhannisyan2.0k

I downloaded the fastq.gz from https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?exp=SRX317694&cmd=search&m=downloads&s=seq. But its usless, its 6GB zipped file..after extraction it is 17GB fastq file. Now I am splitting into paired ends using: fastq-dump --split-3 SRR925687. It is taking very long time. But I understood, should have directly used fastq-dump --split-3 SRR925687 command instead of downloading from the web.

ADD REPLYlink written 2.3 years ago by shuksi198460

The speed of downloading obviously depends on internet connection. But to speed up fetching you can use aspera https://www.ncbi.nlm.nih.gov/books/NBK242625/

ADD REPLYlink written 2.3 years ago by grant.hovhannisyan2.0k
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