how to use dindel

libiyagirl · 01-27-2011, 01:17 PM

hello, I'm new to the bioinformatics, but my first job is using dindel. On the manual it says: "dindel --analysis getCIGARindels --bamFile sample.bam \
--outputFile sample.dindel_output --ref ref.fa". Are these commands? How to run it? Should I input these in Unix? Please bear my stupid question! Thanks a lot!

gprakhar · 01-27-2011, 01:27 PM

What is the data you have and in which format??

libiyagirl · 01-27-2011, 01:43 PM

I have the BAM file and reference file (.fai) !

gprakhar · 01-27-2011, 01:48 PM

Dindel is composed of three steps,
First it extracts the possible InDels from your Input file, which should be a BAM file.
Then it creates windows out of these InDels, this is important for the next step.
After this all the Windows created in last step are realigned.
Finally they are merged in last step.

Yes you will have to do all this on Unix or Linux command line. No other options for running Dindel.

or most of the other programs in NGS pipeline.
The part you quoted is just how to run the first step of Dindel. In that, "dindel" is the program name and rest all are the parameters passed to it.

--
Hope this was helpful.

libiyagirl · 01-27-2011, 01:49 PM

I mean in unix when I type dindel, it just says no such command.

libiyagirl · 01-27-2011, 02:00 PM

I also typed $ ./dindel_x86-64, it also said command not found.....

gprakhar · 01-27-2011, 02:02 PM

Dindel is a program, which you will have to install yourself, via the command line.

But leave that part for the time being, first please read this book on Linux.
Its very easy, short and will be a good time investment for you.
http://groups.google.com/group/unix-...for-biologists

After you complete reading it, then read this post on Seqanswers
http://seqanswers.com/forums/showthread.php?t=4589

--
prakhar gaur

gprakhar · 01-27-2011, 02:16 PM

Sorry, I just checked the link for the book is not working.
Here is the the link to the pdf.
http://korflab.ucdavis.edu/Unix_and_...erl_v2.3.6.pdf

Hope you Enjoy it.
--
prakhar gaur

libiyagirl · 01-27-2011, 02:20 PM

Hi thank you very much for your files. They are very helpful. I'm pretty sure I installed dindel already, but I will double check. Thank you very much for your help!

gprakhar · 01-27-2011, 02:29 PM

On the website, they have both binaries and source code.
How did you install it?
If it did get installed properly then, you should be able to get some error message on executing it.
$./dindel
Error: One of the following options was not specified: --ref --tid or --outputFile

If this is the case with you, then at least the program is installed properly.

libiyagirl · 01-28-2011, 08:45 AM

Thank you very much. I installed the program and now I can use it properly. But still, the first command seems not working. So I used BAM file and FA file, but it said build FASTA index, open: no such file or directory. And it even failed to open the reference file. But these files work fine in the samtools. Any solution?

libiyagirl · 01-28-2011, 09:58 AM

Problem solved! The thing was I did not put the path to the file. But now it works. Thank you!

clarissaboschi · 07-25-2012, 04:04 AM

Which one should I install: the binaries or source code?
I downloaded the binaries for Unix, with many of python scripts, and using the command in the manual, did not work.
Some people said to me that I dont need to instal Dindel, I am confusing..!!!!
I know how to install in Unix, but I dont know if I need and which one I should download!

Thanks

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01-27-2011, 01:17 PM	#1
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	how to use dindel hello, I'm new to the bioinformatics, but my first job is using dindel. On the manual it says: "dindel --analysis getCIGARindels --bamFile sample.bam \ --outputFile sample.dindel_output --ref ref.fa". Are these commands? How to run it? Should I input these in Unix? Please bear my stupid question! Thanks a lot!

01-27-2011, 01:27 PM	#2
gprakhar Member Location: India Join Date: Aug 2010 Posts: 78	What is the data you have and in which format??

01-27-2011, 01:43 PM	#3
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	I have the BAM file and reference file (.fai) !

01-27-2011, 01:48 PM	#4
gprakhar Member Location: India Join Date: Aug 2010 Posts: 78	Dindel is composed of three steps, First it extracts the possible InDels from your Input file, which should be a BAM file. Then it creates windows out of these InDels, this is important for the next step. After this all the Windows created in last step are realigned. Finally they are merged in last step. Yes you will have to do all this on Unix or Linux command line. No other options for running Dindel. or most of the other programs in NGS pipeline. The part you quoted is just how to run the first step of Dindel. In that, "dindel" is the program name and rest all are the parameters passed to it. -- Hope this was helpful.

01-27-2011, 01:49 PM	#5
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	I mean in unix when I type dindel, it just says no such command.

01-27-2011, 02:00 PM	#6
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	I also typed $ ./dindel_x86-64, it also said command not found.....

01-27-2011, 02:02 PM	#7
gprakhar Member Location: India Join Date: Aug 2010 Posts: 78	Dindel is a program, which you will have to install yourself, via the command line. But leave that part for the time being, first please read this book on Linux. Its very easy, short and will be a good time investment for you. http://groups.google.com/group/unix-...for-biologists After you complete reading it, then read this post on Seqanswers http://seqanswers.com/forums/showthread.php?t=4589 -- prakhar gaur

01-27-2011, 02:16 PM	#8
gprakhar Member Location: India Join Date: Aug 2010 Posts: 78	Sorry, I just checked the link for the book is not working. Here is the the link to the pdf. http://korflab.ucdavis.edu/Unix_and_...erl_v2.3.6.pdf Hope you Enjoy it. -- prakhar gaur

01-27-2011, 02:20 PM	#9
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	Hi thank you very much for your files. They are very helpful. I'm pretty sure I installed dindel already, but I will double check. Thank you very much for your help!

01-27-2011, 02:29 PM	#10
gprakhar Member Location: India Join Date: Aug 2010 Posts: 78	On the website, they have both binaries and source code. How did you install it? If it did get installed properly then, you should be able to get some error message on executing it. $./dindel Error: One of the following options was not specified: --ref --tid or --outputFile If this is the case with you, then at least the program is installed properly.

01-28-2011, 08:45 AM	#11
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	Thank you very much. I installed the program and now I can use it properly. But still, the first command seems not working. So I used BAM file and FA file, but it said build FASTA index, open: no such file or directory. And it even failed to open the reference file. But these files work fine in the samtools. Any solution?

01-28-2011, 09:58 AM	#12
libiyagirl Member Location: canada Join Date: Jan 2011 Posts: 27	Problem solved! The thing was I did not put the path to the file. But now it works. Thank you!

07-25-2012, 04:04 AM	#13
clarissaboschi Member Location: US Join Date: Apr 2010 Posts: 63	Which one should I install: the binaries or source code? I downloaded the binaries for Unix, with many of python scripts, and using the command in the manual, did not work. Some people said to me that I dont need to instal Dindel, I am confusing..!!!! I know how to install in Unix, but I dont know if I need and which one I should download! Thanks