Entering edit mode
8.2 years ago
torkel.loman
▴
10
I'm currently writing a program to which the input is a .sam file. Now to try a few things out I want to use a sample .sam file. I have used a simple one I made up myself, but I would want one from real data (preferably sorted).
I have looked around but I have only found sample .bam files. My problem is that I have been unable to get samtools to work (and believe be I have tried). I have also been unable to get other similar tools like Picard to work. This means that I'm unable to convert .bam to .sam.
Do anyone know were you can find such sample .sam files?
Wouldn't it be more interesting to fix your samtools issue? Installation of that shouldn't be too hard. What's going wrong?
as @WouterDeCoster said post the error that you got specially that for tool like Picard you only need Java to make it work and it is straightforward, To report an error you need to post your operating system version , the error you have ,
reefer to
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
http://stackoverflow.com/help/how-to-ask
Basically samtools requires some program to do something. However, the computers to which I have had acess won't permit me to install that programs that samtool needs.
I spent almost 6 weeks this spring trying to bypass it before I gave up.
(I have some hopes that I will get acess to a computer able to run samtools in a few weeks. Hopefully)
Okay, if you remain that vague you shouldn't expect any help. Samtools should be an easy installation, if that doesn't work on your system then you need to fire your sysadmin. 6 weeks is ridiculously long for an installation that is so common...
(Samtools is a long story, to begin with I were not supposed to have acess to any linux computer (for some reason their use were very restricted) and when I got acess to one the sysadmins were very reluctant to let me add any kind of program (at least I managed to get the BWA-MEM mapper to work).)
Long story short is that I have no samtools but that is another problem. The only reason that I mentioned samtools is due to that problem I need to find some sample file not in the .bam format rather I am looking for one in the .sam format (there are some topics here already but all recommended there are in the .bam format)
(on the samtools issue, things are changing here and I should be able to run it in a few weeks)
You can find an example sorted sam file here. You would need to be able to access github.com.
Are you able to run java on your computer? If so you may be able to use igvtools from IGV to sort sam files. See this page for example data.
Thank you very much! Just what I needed!
(Thanks for the IGV tips as well. I run Java but did not know about it. Will look into it)
what @WouterDeCoster said : what is the problem with samtools ?