Question: hello i know i must accept that im a stupid
0
gravatar for jivarajivaraj
4.0 years ago by
jivarajivaraj40 wrote:

I should work with Rseq data with bowtie2

I tried these steps but at last it says "bowtie2-builds exe is not recognized as an external or internal and operable command or batch file"

I cried a lot because its too difficult accepting this reality that im a stupid and I should change my route in life from bioinformatics to something else…

I tried windows 8

32 bit

64bit

Even I tired tdm gcc as compiler and mingw.org but in between I got confused

Step 1) Download this package: http://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.2.4/bowtie2-2.2.4-mingw-win64.zip/download

Step 2) Unzip it. Place it in a folder you can navigate to, something simple, such as C:\bowtie2_win64

Step 3) Assuming you have windows 7 (you should say what operating system you are using), open "cmd.exe", this is command prompt, you can open it by pressing WindowsKey+R and typing cmd.exe + enter

Step 4) In command prompt (black windows), navigate to where you have unzipped your bowtie, in Step2 I told you to put it in C:\bowtie2_win64, so write in command prompt "cd C:\bowtie2_win64".

Now you need to test whether the precompiled windows binary works for you, so:

Step 5) Index example fasta file, type "bowtie2-build-s.exe example/reference/lambda_virus.fa lambda_virus

Step 6) If all goes well, next you need to align the sample reads provided "bowtie2-align-s.exe -x lambda_virus -U example/reads/reads_1.fq -S eg1.sam"

If all went well, you should see:

10000 reads; of these:

  10000 (100.00%) were unpaired; of these:

    596 (5.96%) aligned 0 times

    9404 (94.04%) aligned exactly 1 time

    0 (0.00%) aligned >1 times

94.04% overall alignment rate

software error • 2.7k views
ADD COMMENTlink modified 4.0 years ago by Daniel3.7k • written 4.0 years ago by jivarajivaraj40
8

I cried a lot because its too difficult accepting this reality that im a stupid and I should change my route in life from bioinformatics to something else…

Don't beat yourself up too badly. Step back from the computer and go outside for a walk. Everyone here has probably had that same feeling at some time. This is a young field with a lot of very tricky problems aside from the core questions. Stick with it and you'll have success!

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Dan D6.6k
3

Hello jivarajivaraj!

We believe that this post does not fit the main topic of this site.

Not a real question

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 4.0 years ago by Michael Dondrup45k
2

Jivaraj,

I would suggest you join a lab. That is where you will find people who have faced similar problems earlier. They can at least show you some direction.

ADD REPLYlink written 4.0 years ago by Nikhil Chaudhary60

you all right here in iran im alone with my problem then i am communicating with a proffesor in max plank for an internship course

thanks for your tip

ADD REPLYlink written 4.0 years ago by jivarajivaraj40

So, does that mean it is working now?

ADD REPLYlink written 4.0 years ago by Michael Dondrup45k
2

no... he copied my instructions to another thread:

please some one help me step by step i was really exhausted

 

ADD REPLYlink written 4.0 years ago by Adrian Pelin2.2k
2

jivarajivaraj:  as Adrian Pelin noted you have now duplicated this question several times.  Please read: How To Ask Good Questions On Technical And Scientific Forums, which addresses how to ask a good question.  

ADD REPLYlink written 4.0 years ago by Zev.Kronenberg11k

im not he im a poor girl, a sad one in a cold midnight from iran

ADD REPLYlink written 4.0 years ago by jivarajivaraj40
5

I can understand your pain. This happens with almost everyone who is a biologist and has just started working with command line based tools. Also, installing these tools and setting up the correct environment can be cumbersome. First of all don't be hard on yourself. Everyone goes through this phase and no research or job is more important than your emotional or mental well-being. I would suggest you to install Ubuntu on your laptop if laptop is the only resource you have. See if you can get some unix-based computational resource at your university. Most of the bioinformatics tools are linux based and it is easy to install and work with them on linux. You can install both windows and ubuntu on your laptop (See here: http://www.everydaylinuxuser.com/2014/05/install-ubuntu-1404-alongside-windows.html). I would advise you to take help of your friend who has already done it. Installing bowtie should be easier on Ubuntu. Again, take it easy and stay positive. 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Ashutosh Pandey11k
2

The easiest way to get started is with BioLinux. It comes with bowtie and any other major bioinformatics tool you can imagine built in. No time and trouble needed to be spent on instalation

http://environmentalomics.org/bio-linux/

ADD REPLYlink written 4.0 years ago by Daniel3.7k

thank you all very much

ADD REPLYlink written 4.0 years ago by jivarajivaraj40
4

There are no tears in bioinformatics!

Only the boys cry.  ;-)

ADD REPLYlink written 4.0 years ago by Michele Busby1.9k
2

Hey! I don't cry!

...much...

ADD REPLYlink written 4.0 years ago by Dan D6.6k

thanks all for ur kindness i will try more and hope a day when im sharing my victory over bowtie!!!

ADD REPLYlink written 4.0 years ago by jivarajivaraj40

hello

thanks adrian

at last i got the same results you mentioned after step (6) for me

 

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by jivarajivaraj40
1

That's amazing! That's how bioinformatics works :) Keep trying and eventually it will work. Now what I gave you was a sample dataset. Now you can try using this to adapt it to your own dataset.

If you have more questions, post them in the previous thread "please some one help me step by step i was really exhausted"

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by Adrian Pelin2.2k

thanks from my heart

because for sure without your step wise guidance i couldnt do my job easily...

ADD REPLYlink written 4.0 years ago by jivarajivaraj40
7
gravatar for Istvan Albert
4.0 years ago by
Istvan Albert ♦♦ 78k
University Park, USA
Istvan Albert ♦♦ 78k wrote:

It is very important to realize early on that bioinformatics (and big data analytics in general) is not just a method or and approach - it is a way to think. Computation == Thought.

The brain needs to get rewired - hence the feeling of helplessness and inadequacy while that happens. This process needs time, it cannot be rushed, the same way you can't learn a language in a week no matter how hard you try. 

The keys are systematic practice, consistency and persistence + give your brain time to adapt. 

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Istvan Albert ♦♦ 78k
3

Also, learn to blame the programmer.

i.e. I can't do this. -> This is hard.  It's not programmed to work easily.

ADD REPLYlink written 4.0 years ago by Michele Busby1.9k
4
gravatar for seta
4.0 years ago by
seta1.1k
Sweden
seta1.1k wrote:

I have no enough familiarity with this tool, yet. but I can say windows is not the suitable system for doing these task for sure, just try linux, it is so much friendly with bioinformatic! 

ADD COMMENTlink written 4.0 years ago by seta1.1k
4
gravatar for Siva
4.0 years ago by
Siva1.6k
United States
Siva1.6k wrote:

As others have suggested, learning to work in the Linux environment is essential if you want to do large scale bioinformatics analyses.

If you don't have access to Linux machines but would like to learn Linux, there are several free online options.

Check this Free Linux server for bio-computing? about free online Linux servers.

Linuxzoo offers free Linux virtual machines with full root access.

There are also several sites that provides free shell accounts. Here's a list of those sites.

You cannot expect privacy on these online free services, so do not upload any sensitive data.

There is a free edX course "Introduction to Linux" beginning next month.

All the best.

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Siva1.6k
3
gravatar for Daniel
4.0 years ago by
Daniel3.7k
Cardiff University
Daniel3.7k wrote:

The easiest way to get started is with BioLinux. It comes with bowtie and any other major bioinformatics tool you can imagine built in. No time and trouble needed to be spent on instalation

http://environmentalomics.org/bio-linux/

Documentation is a little out of date, but can be found at http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl7_latest.pdf

ADD COMMENTlink modified 4.0 years ago • written 4.0 years ago by Daniel3.7k
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