a few question about galaxy

[rafi bondi]

i got 4 big sra files. two of them are ~1.5 Gb and two other ~5Gb.
the guy who gave it to me told me he gave me 10 Exon Genome's of different people.
i want to go over the sequence and look for changes in certain genes.
at the beginning i wanted to work with galaxy but because uploading the file took long i installed the galaxy on my computer.
but the galaxy can't fetch the files from the HD.
i downloaded the toolkit but couldn't find a tool the convert from SRA to SAM.
i'm looking for a way to take separate the sra file so i can take only the genes i want and look for differences between the different genomes.

[maubp]

By SRA format, do you mean files from the NCBI's Sequence Read Archive (once called the Short Read Archive)?

http://www.ncbi.nlm.nih.gov/sra/

[rafi bondi]

yes

those are the files

[maubp]

When you say "convert" from SRA to SAM, you probably want to map the reads onto a reference genome.

Most mapping tools do FASTQ to SAM, so I'd start by getting the reads as FASTQ (perhaps by downloading the reads as FASTQ from the SRA website). You'll also need the reference genome in FASTA format.

[rafi bondi]

i have only those 4 files with sra extension.
i know i need to map them but whitch tool can i use?
i got a tool called sra-dump but i didn't quite understand how to use it.

[ntremblay]

He'res some information from the sra-dump instructions (http://www.ncbi.nlm.nih.gov/books/NBK49294/):

3.3 Example:

toolkit installed in: /gold/sra/bin64/

downloaded SRR (contains directory 'col' and files md5, meta, sealed... ) in: /gold/sra/download/SRR000299/

command to convert the SRA object into fastq data would be:

/gold/sra/bin64/fastq-dump -A SRR000299 -D /gold/sra/download/SRR000299/
Output will be ‘SRR000299.fastq’ in current directory

This will also work for single-file SRA archives (example SRR000299.sra or SRR000299.lite.sra) using the single file as the directory.

/gold/sra/bin64/fastq-dump -A SRR000299 -D /gold/sra/download/SRR000299.sra

So the syntax to use the program is .../fastq-dump -A <SRR_accession> -D <Path_to_SRR_Directory> -O <Output_Path>

it should work like a charm

[kmcarr]

Why don't you just download the fatq files directly from the SRA instead of bothering with the conversion?

Nov 29:

O.K., I get it now. I haven't been to SRA in a little while so I didn't realize they have entirely switched from providing FASTQs to only SRA files.

[nekrut]

Rafi:

We just enabled an upload through an ftp. Take a look at the instructions at the upload interface. Let me know if you have issues.