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Old 05-03-2011, 04:18 AM   #1
papori
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Default SRA format

Hey,
when i am have SRA format. (from Sequance Read Archive)
i extract it to fastq.
then i have 3 new files
******_1.fastq
******_2.fastq
*********.fastq

what is the different?

Thank...
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Old 05-03-2011, 05:17 AM   #2
brpet
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Quote:
When executing the ‘fastq-dump’ utility, the complete path to the utility must be used unless the utility can be located using the current Linux path environmental variable. In its simplest form, the ‘fastq-dump’ utility executes as follows:

fastq-dump <accession archive>

Tthe ‘accession archive’ must be located in the current working directory. For example, with SRA format data for SRR000001 in the current working directory:

fastq-dump SRR000001

In this case, the result will be the creation of three files in the same directory:

SRR000001.fastq

SRR000001_1.fastq

SRR000001_2.fastq

The file, ‘SRR000001.fastq’, contains fragment read sequences where only a single biological/application read exists (or remained after filtering) for a spot.

The file, ‘SRR000001_1.fastq’, contains the first read in spots containing paired reads and the file, ‘SRR000001_2.fastq’, contains the second read.
Read the manual...
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Old 05-11-2011, 06:47 AM   #3
papori
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Default

thanks,
if i am having for example data from experiment as in this link..

http://trace.ncbi.nlm.nih.gov/Traces...m=search&s=seq


all of the 6 are different samples?
SRR037689
SRR037690
SRR037691
SRR037692
SRR037693
SRR037694
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Old 05-11-2011, 12:38 PM   #4
kmcarr
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Quote:
Originally Posted by papori View Post
thanks,
if i am having for example data from experiment as in this link..

http://trace.ncbi.nlm.nih.gov/Traces...m=search&s=seq


all of the 6 are different samples?
SRR037689
SRR037690
SRR037691
SRR037692
SRR037693
SRR037694
No, they are not necessarily different samples. They are six separate runs (SRR = run accession number). A single sample may be run more than once. You would need to look at the details for each run to see which sample it includes and if they are the same or different. Samples have accession numbers starting with SRS. There may also be more experiments (SRX) associated with this sample. The general hierarchy is:

A study (aka project: SRP) has one or more samples.
A sample has one or more experiments.
An experiment has one or more runs.
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