Compare hisat2 and tophat

[zhanghao]

I tried to used hisat2 to instead of tophat2 and compared the results. As shown in the picture (attachment) in IGV, there are many grey lines in the hisat2 result (upper one), means many reads were seperated with long distance. But the tophat result (below) is better. I try to add the parameter "--known-splicesite-infile <path>" to provide a splice sites in the mapping step, but it is useless, the same result was got. How to resolve this problem? Could anyone help me about it? I want to get similar result as tophat. I really love hisat2, it runs so fast and can save much time, also it can run on my old PC.
Thank you very much!

[zhanghao]

the picture

[zhanghao]

picture in this floor

[Brian Bushnell]

The hisat results do look odd, though that doesn't mean they're wrong. You might compare to a 3rd mapper like BBMap to get a tie-breaking opinion.

[dpryan]

We've occasionally seen some really odd results with hisat2 that looked more as expected with other aligners (namely, BBMap), so as Brian said give that a try. I've begun suspecting that there are a few bugs that need worked out in hisat2 still.

[zhanghao]

The hisat results do look odd, though that doesn't mean they're wrong. You might compare to a 3rd mapper like BBMap to get a tie-breaking opinion.

I found bbmap plugin in generous, so I can do it with geneious and compared them.

[GenoMax]

Or just get BBMap directly: http://sourceforge.net/projects/bbmap/ Plugin in geneious may not be the latest version.

[zhanghao]

Or just get BBMap directly: http://sourceforge.net/projects/bbmap/ Plugin in geneious may not be the latest version.

I install bbmap according to the readme file. But when I run bbmap.sh, it showed "commond not found". I do not know why? I checked the java using java -version, java8 has been installed. Could you help me about this? @Brian Bushnell

[GenoMax]

Add execute permissions to bbmap script.

$ chmod a+x /path_to/bbmap.sh

[zhanghao]

Add execute permissions to bbmap script.

$ chmod a+x /path_to/bbmap.sh

chmod can not resolve this problem. It is useless!

[zhanghao]

my operating system is ubuntu 14.04

[GenoMax]

chmod can not resolve this problem. It is useless!

You need to provide additional information as to why you think it is "useless". Did you get the same error? Can you show us permissions on bbmap.sh (hopefully you replaced the "path_to" part with real path for your system)?

$ ls -l /path_to/bbmap.sh

If you are not able to get the shell script to work then run the program directly with java as described by Brian in the first post here: http://seqanswers.com/forums/showthread.php?t=41057

[Brian Bushnell]

Can you show us permissions on bbmap.sh (hopefully you replaced the "path_to" part with real path for your system)?

$ ls -l /path_to/bbmap.sh

Yes, I think this is a common mistake. BBMap does not really have an installer, you just unzip it. If you unzipped it to /usr/bin/bbmap/ then you would type /usr/bin/bbmap/bbmap.sh.

But I imagine the Geneious plugin would be easier, if you are used to Geneious.

[zhanghao]

Yes, I used the real path /home/lydia/bbmap/bbmap.sh. And when I run bbmap, I just cd to the bbmap folder and type bbmap.sh.

[blancha]

I just cd to the bbmap folder and type bbmap.sh

If the current folder is not in your path, the previous command won't work.
Try this command, instead after doing cd to the bbamp folder.

./bbmap.sh

You can also add the current folder to your PATH.
To make the change permanent, add the command to your ~/.bash_profile file and restart the terminal, or source the ~/.bash_profile file.

export PATH =.:$PATH