hello I know I must accept that im a stupid

Question

[jivarajivaraj]

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

[Dan D]

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!

[Michael]

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!

[Nikhil Chaudhary]

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.

[jivarajivaraj]

you are right, here in Iran I'm alone with my problem then I am communicating with a professor in max planck for an internship course

thanks for your tip

[Michael]

So, does that mean it is working now?

[Adrian Pelin]

No... he copied my instructions to another thread: please some one help me step by step i was really exhausted

[Zev.Kronenberg]

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.

[jivarajivaraj]

I'm not he, I'm a poor girl, a sad one in a cold midnight from Iran

[Ashutosh Pandey]

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.

[Daniel]

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 installation

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

[jivarajivaraj]

thank you all very much

[Michele Busby]

There are no tears in bioinformatics!

Only the boys cry. ;-)

[Dan D]

Hey! I don't cry!

...much...

[jivarajivaraj]

Thanks all for your kindness I will try more and hope a day when I'm sharing my victory over bowtie!!!

[jivarajivaraj]

hello

thanks adrian

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

[Adrian Pelin]

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

[jivarajivaraj]

Thanks from my heart because for sure without your step wise guidance I couldn't do my job easily...

Answer 1

[Istvan Albert]

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.

[Michele Busby]

Also, learn to blame the programmer.

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

Answer 2

[seta]

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!

Answer 3

[Siva]

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 thread 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.

Answer 4

[Daniel]

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 installation

Documentation is a little out of date, but can be found at http://nebc.nerc.ac.uk/downloads/courses/Bio-Linux/bl7_latest.pdf