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I want to find a RNA-Seq dataset for C. Elegans to use it in RNA-Skim software. For those who does not know RNA-Skim let me explain it a bit. It is a tool which is used to quantify RNA-Seq data using sig-mers(special kind of k-mer). Firstly RNA-Skim clusters protein coding genes and find substrings that are special to cluster of that gene. After this preperation stage, it takes an RNA-seq data as an input and tries to quantify transcripts in it. So, I need to find a dataset in fasta file format for this step. Since I'm pretty new in this area, is there anyone who could provide me information about how could I find it? Complete information about RNA-skim can be found here : RNA_SKIM

EDIT The type of a dataset I'm looking for is something like that: http://codepad.org/n3ioT3nj .This dataset is for mouse, I need to find such a dataset for C. elegans as I said before

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    $\begingroup$ Try any of these: www.wormbase.org, www.modencode.org, data.modencode.org, or ftp.modencode.org. Also, they won't be fasta files for NGS data they will either be fastq format or SAM/BAM format $\endgroup$ – mdperry May 1 '15 at 23:48
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Go to NCBI-SRA or GEO and search for RNAseq data. Set organism as C. elegans and optionally any other keywords that you are interested in. This search term will give you all RNAseq data in SRA from C. elegans:
("caenorhabditis elegans"[Organism]) AND "strategy rna seq"[Properties]
You will generally find files in fastq format which you can easily convert to fasta. There are many tools that do that; you can also do it with your own script. Following awk command will do the job:

awk 'NR%4==1{print ">"substr($0,2)} NR%4==2{print}' data.fastq > data.fasta

Apart from SRA you can also look at ENA (European Nucleotide Archive) and DDBJ

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    $\begingroup$ SRA is the right place for sequencing data. GEO will have all kinds of expression data. In SRA you just have to click on a particular run and find the experiment ID (Starts with SRX). Paste it in this page and download the data. $\endgroup$ – WYSIWYG May 8 '15 at 8:54
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    $\begingroup$ @stackunderflow In the GEO page when you click on one of the experiments you will get a SRA link at the end of the page. You can click on that (ftp link) and download your file. But these will be in .sra format which you have to convert to .fastq. .sra files are smaller and will download faster and you can use fastq-dump of sra-toolkit to convert sra to fastq. Or else paste the experiment ID in the second link that I mentioned in the previous comment. $\endgroup$ – WYSIWYG May 8 '15 at 9:00
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    $\begingroup$ @stackunderflow Paired end sequencing data has 2 files and reads in one file will have the suffix "1" in the header while the other will have "2". $\endgroup$ – WYSIWYG May 12 '15 at 5:20
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    $\begingroup$ @stackunderflow These are replicates of the samples. Sometimes same sample is loaded twice and you have two runs for the same sample. This is not the case here. Rep1 is one sample and Rep2 is another sample for the same experimental protocol. If you read the paper corresponding to the data you will understand. See the study summary (click more). $\endgroup$ – WYSIWYG May 15 '15 at 5:39
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    $\begingroup$ @stackunderflow two runs of the same sample will be under the same experiment SRX but the biological replicates will usually have a different experiment ID. These things are usually described in the summary $\endgroup$ – WYSIWYG May 15 '15 at 20:50

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