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Old 11-07-2015, 06:59 PM   #1
zhanghao
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Default Compare hisat2 and tophat

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!
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Last edited by zhanghao; 11-07-2015 at 07:39 PM.
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Old 11-07-2015, 07:05 PM   #2
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the picture
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Old 11-07-2015, 07:25 PM   #3
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picture in this floor
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Old 11-07-2015, 08:31 PM   #4
Brian Bushnell
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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.
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Old 11-08-2015, 02:39 AM   #5
dpryan
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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.
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Old 11-08-2015, 04:48 AM   #6
zhanghao
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Quote:
Originally Posted by Brian Bushnell View Post
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.
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Old 11-08-2015, 05:36 AM   #7
GenoMax
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Or just get BBMap directly: http://sourceforge.net/projects/bbmap/ Plugin in geneious may not be the latest version.
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Old 11-08-2015, 07:30 AM   #8
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Quote:
Originally Posted by GenoMax View Post
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

Last edited by zhanghao; 11-08-2015 at 07:35 AM.
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Old 11-08-2015, 07:33 AM   #9
GenoMax
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Add execute permissions to bbmap script.

Code:
$ chmod a+x /path_to/bbmap.sh
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Old 11-08-2015, 07:41 AM   #10
zhanghao
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Quote:
Originally Posted by GenoMax View Post
Add execute permissions to bbmap script.

Code:
$ chmod a+x /path_to/bbmap.sh
chmod can not resolve this problem. It is useless!
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Old 11-08-2015, 07:47 AM   #11
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my operating system is ubuntu 14.04
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Old 11-08-2015, 08:29 AM   #12
GenoMax
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Quote:
Originally Posted by zhanghao View Post
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)?

Code:
$ 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
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Old 11-08-2015, 11:06 AM   #13
Brian Bushnell
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Quote:
Originally Posted by GenoMax View Post
Can you show us permissions on bbmap.sh (hopefully you replaced the "path_to" part with real path for your system)?

Code:
$ 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.
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Old 11-08-2015, 05:13 PM   #14
zhanghao
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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.
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Old 11-08-2015, 06:00 PM   #15
blancha
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Quote:
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.

Code:
./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.

Code:
export PATH =.:$PATH
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Old 04-07-2016, 03:56 AM   #16
nlapalu
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Hi,

Did you try to test an index like described :

--known-splicesite-infile <path>



With this mode, you can provide a list of known splice sites, which HISAT2 makes use of to align reads with small anchors.
You can create such a list using python hisat2_extract_splice_sites.py genes.gtf > splicesites.txt, where hisat2_extract_splice_sites.py is included in the HISAT2 package, genes.gtf is a gene annotation file, and splicesites.txt is a list of splice sites with which you provide HISAT2 in this mode. Note that it is better to use indexes built using annotated transcripts (such as genome_tran or genome_snp_tran), which works better than using this option. It has no effect to provide splice sites that are already included in the indexes.
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Old 08-24-2016, 01:08 AM   #17
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have you change the paramter "--max-intronlen" to limit the maximum intron length?
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