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Old 04-02-2011, 12:55 PM   #1
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Default BFAST: Need "Phi X 174" file example dataset

Hi all,

I am trying to download an example data set for BFAST, which is Phi X 174 from the BFAST main page but the link is broken. [http://sourceforge.net/apps/mediawik...tle=Main_Page]


If anyone has already downloaded this dataset before, or knows about another link from which I can download this dataset, please help me attaching the file to this thread or pointing me to another link.


Thanks..
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Old 04-02-2011, 03:20 PM   #2
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Sorry, it has been taken down.
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Old 04-02-2011, 08:57 PM   #3
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Thanks Nils for your reply.
Why it has been taken down?

If it is not possible to get it, could you please point me to another similar data set which I can use to run the same example in the BFAST manual [Chapter 7]?

Thanks..
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Old 04-02-2011, 09:29 PM   #4
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This post was not removed. Your repost was.
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Old 04-02-2011, 10:47 PM   #5
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Nils and I meant the files which have been taken down, not the post.

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Old 04-03-2011, 01:28 AM   #6
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The files are not available as I have left UCLA. I will remove the example from the manual to avoid future confusion. Therefore, there is no example.

Last edited by nilshomer; 04-03-2011 at 01:31 AM.
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Old 04-03-2011, 02:32 AM   #7
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Thanks Nils for your reply.

So, if I want to run an example to try the BFAST code, from where I can get a similar data set sample??

Thanks..
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Old 04-03-2011, 12:13 PM   #8
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Quote:
Originally Posted by CS Student View Post
Thanks Nils for your reply.

So, if I want to run an example to try the BFAST code, from where I can get a similar data set sample??

Thanks..
The short read archive or short read simulators (see wgsim in SAMtools). Search around, you should find some.
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Old 04-03-2011, 12:36 PM   #9
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Many thanks for your replies Nils, appreciated.

As far as I understood from the example explanation, I need a reference genome in FASTA format data in addition to the short read files.

I am very new in using the BFAST tool, and as a start I would prefer to use the same data pointed by the manual, especially that the expected output files are available in the BFAST source code. This will be very useful for me to compare the output of my first try to run the BFAST code with the expected output.

Is it possible to attach the "Phi X 174" zip file to this thread?

Thanks..
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Old 04-03-2011, 12:40 PM   #10
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Nope, they no longer exist. Sorry that I cannot be of more help.
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Old 04-03-2011, 11:32 PM   #11
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There are PhiX samples in SRA, for example:

http://www.ncbi.nlm.nih.gov/sra/SRX037794?report=full

The PhiX genome sequence is available under the accession NC_001422. Hopefully between these you should have something to work with.
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