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Old 10-30-2011, 08:37 PM   #1
roshanpatel95
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Location: san francisco

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Default Newbie Help

Hey guys,
This is a newbie question, but really having hard time setting up Bowtie and would really appreciate if someone helps me through this. I did read the tutorial on the website, but everytime i put the code in terminal or windows command prompt, just gives me an error.

Could someone explain how to get Bowtie or Bowtie 2 started?
Thanks for your help in advance.
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Old 10-30-2011, 10:14 PM   #2
ETHANol
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Nobody can explain to you better then the program documentation because no one knows what you did, what error messages you get, what machine you have, you operating system, etc.

You need to spend the time and create a very detailed and clear post.

Some say there's no such thing as a stupid question. Those people are idiots. It all comes down to asking the right question(s) in the right way.

Good luck.
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Old 10-30-2011, 11:19 PM   #3
roshanpatel95
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I know it sounds stupid, but i really need to get this program started.

I am using windows 7 and using windows command prompt. I downloade Bowtie binary from their website and it said to issue the command (i was lost right here...am i supposed to write a command in CMD or is there a program that i need to get).

what i did so far is, uncompressed the binary and opened CMD and got to the folder by using the cd 'foldername" and i am assuming this is where " bowtie e_coli reads/e_coli_1000.fq" command but it keeps giving me an error saying "is not recognized as an internal or external
command, operable program or batch file"

here is the bowtie tutorial website http://bowtie-bio.sourceforge.net/tutorial.shtml

thnx for the help
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Old 10-31-2011, 02:17 AM   #4
gringer
David Eccles (gringer)
 
Location: Wellington, New Zealand

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if you don't have bowtie in your path, then you need to access it using relative file names ('"c:\bowtieDirectory\bowtie" "e_coli reads\e_coli_1000.fq"'). The tutorial was designed for people to use it on a GNU/Linux system, which is why there are forward slashes in the file names. If you're going to be doing command-line bioinformatics, I would seriously consider getting a Linux computer set up for use.
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Old 10-31-2011, 04:37 AM   #5
Bioinfo_MD
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Quote:
Originally Posted by gringer View Post
if you don't have bowtie in your path, then you need to access it using relative file names ('"c:\bowtieDirectory\bowtie" "e_coli reads\e_coli_1000.fq"'). The tutorial was designed for people to use it on a GNU/Linux system, which is why there are forward slashes in the file names. If you're going to be doing command-line bioinformatics, I would seriously consider getting a Linux computer set up for use.
And I suggest you start learning some Unix because to do extensive Next Gen Sequencing analysis you will need it.

A very good starting point as many in this forum has mentioned is the "Unix and Perl Primer for Biologists" from this link:
http://korflab.ucdavis.edu/Unix_and_Perl/
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Old 10-31-2011, 07:39 AM   #6
roshanpatel95
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thnx for the help
much appreciated.
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