BFAST: Need "Phi X 174" file example dataset

CS Student · 04-02-2011, 01:55 PM

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..

nilshomer · 04-02-2011, 04:20 PM

Sorry, it has been taken down.

CS Student · 04-02-2011, 09:57 PM

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..

ECO · 04-02-2011, 10:29 PM

This post was not removed. Your repost was.

CS Student · 04-02-2011, 11:47 PM

Nils and I meant the files which have been taken down, not the post.

Thanks..

nilshomer · 04-03-2011, 02:28 AM

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.

CS Student · 04-03-2011, 03:32 AM

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..

nilshomer · 04-03-2011, 01:13 PM

Quote:

Originally Posted by CS Student

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.

CS Student · 04-03-2011, 01:36 PM

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..

nilshomer · 04-03-2011, 01:40 PM

Nope, they no longer exist. Sorry that I cannot be of more help.

simonandrews · 04-04-2011, 12:32 AM

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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04-02-2011, 01:55 PM	#1
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	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..

04-03-2011, 02:28 AM	#6
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	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 02:31 AM.

04-02-2011, 04:20 PM	#2
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Sorry, it has been taken down.

04-02-2011, 09:57 PM	#3
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	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..

04-02-2011, 10:29 PM	#4
ECO --Site Admin-- Location: SF Bay Area, CA, USA Join Date: Oct 2007 Posts: 1,358	This post was not removed. Your repost was.

04-02-2011, 11:47 PM	#5
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	Nils and I meant the files which have been taken down, not the post. Thanks..

04-03-2011, 03:32 AM	#7
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	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..

04-03-2011, 01:36 PM	#9
CS Student Member Location: US Join Date: Apr 2011 Posts: 20	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..

04-03-2011, 01:40 PM	#10
nilshomer Nils Homer Location: Boston, MA, USA Join Date: Nov 2008 Posts: 1,285	Nope, they no longer exist. Sorry that I cannot be of more help.

04-04-2011, 12:32 AM	#11
simonandrews Simon Andrews Location: Babraham Inst, Cambridge, UK Join Date: May 2009 Posts: 871	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.