Can anyone suggest me a software or tools that I can use to view bam files on windows and edit them? Something that can also help creating bai files for each bam file... I want it to work on windows... Thanks a lot
Since most bioinformatics tools run on Unix, working in Windows will severely limit what you can do.
You can try Galaxy to see if there's a tool for creating indices but I've never tried uploading large files for analysis in there.
Seqmonk has a Windows version and will let you view mapped .bam files.
It would be well worth the effort to familiarise yourself with Unix. Just look for a short introductory course to get yourself started.
Well, the data are confidential so I can't upload them on galaxy... so galaxy is out of my options... I guess all ways end to linux :) yeah I have started learning it but if there were a windows solution, that would be easier... Does seqmonk let you edit format of chromosomes on bam files? Thanks a lot for your assistance
While entirely not an answer to your question, https://www.codecademy.com/ has a short interactive course for beginners to learn the basic usage of linux command line.
Maybe learning a new operating system is a little painful at first, but it will quickly become a big plus.
Well, in fact there are solutions for Windows, they are just more expensive. It all boils down to money.
For example, you could buy and learn MATLAB and some other expensive user-friendly Windows tools; you will need to buy a powerful Windows desktop workstation instead of using a shared Linux computer cluster, etc. Note that learning MATLAB might be a similar problem as learning a new operating system, so there are really no easy solutions.
So, in a way your local bioinformatician was technically not wrong when saying that there is nothing you can't do on Windows that you can do on Linux.
MATLAB is ok... I can have that software... but as you've mentioned, I will need to spend time on learning it... I've found an R package for samtools... if it can fulfill my needs, that would be nice... otherwise I will move to Linux which was suggested by most of members here... thanks a lot :)
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It sounds like you're still having troubles getting started with Linux/Galaxy/samtools, huh? :( Whats worse, its clear from your post history that you are really reading around the subject and are trying very hard (unlike some people...) to do this right.
Whilst i'm sure Window's solutions exist for creating bai files (i.e., indexing your sorted bams), the more you go towards working in Windows, the less the Biostars community will be able to help you later on with more complicated things, because most of the tools for working with these files only run on linux and mac. If you can get your hands on an Apple Mac, that's probably going to be the easiest route. How far did you get in the end with Biolinux? If you go to the Biolinux website (http://environmentalomics.org/bio-linux-installation/) they have a "Running Bio-Linux as a VM with VirtualBox" section that will let you run Biolinux from inside Windows if you want to try that first. If you can get Biolinux up and running, the command to sort and index your BAM files are just 2 lines, and you will have all the other tools to view/edit your data at your fingertips.
If all you have to do for your whole project is just sort and index a BAM file, then perhaps you don't need Linux - but what good is a sorted and indexed BAM file if you cant do anything with it? :)
Haha :)) yeah you are right... I've started working on linux and I have learned some basic commands on terminal and also I can understand samtools commands better now... as you say there is not a better way and linux is the only choice... I have also downloaded biolinux to install on VMware and haven't started learning it yet for being busy... All my tries had been on Ubuntu but I will soon move to biolinux to see how it is... My main plan is to detect CNVs using CODEX which can run on windows but it requires bam files(along with bai files) and a bed file... And since bai files are not provided, I need to create them... Thanks a lot for your assistance...
Oh, if you got Ubuntu working then perhaps stick with that and dont worry about Biolinux - you're on the right track! :D Usually people learn Linux by making it their day-to-day personal computer, and then learning the terminal stuff bit-by-bit after their familiar with being productive in linux for email/web, etc. Slowly, in other words.
The statement "theres nothing that cant be done on Windows" is just not true - unless running Linux via VMWare in windows counts. Sometimes, there are literally no tools that do the job other than tools written for linux/mac.
I understand it... So I shouldn't worry about biolinux? Good news :) ... Thanks a lot for your time and energy to help me
If you have a linux machine with Samtools installed, creating a bam index is very easy.
Type two commands on the terminal and you're done.
samtools sort test.bam test_sorted
samtools index test_sorted.bam test_sorted.bai
I somehow understand these commands but I'm not sure how to import the files in the commands and save the output bai files... If I ask someone familiar with linux commands, would it be easy for him/her to work with these commands even though he/she hasn't worked with samtools? If yes, I can get help from them
Yes, get your friend to show you. It will be very easy to understand once you see an example.
Sure... Thanks a lot
There are options that will work on windows but unfortunately they are NOT free/open source. If your budget allows for it take a look at CLC Genomics Workbench (you can pretty much do all common NGS analyses with this) or Geneious.
Thank youuuuuu... Good windows solutions can be much more of interest...