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Old 11-07-2015, 05:59 PM   #1
zhanghao
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Location: BEIJING

Join Date: Nov 2015
Posts: 17
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!
Attached Images
File Type: jpg igv1.jpg (84.2 KB, 82 views)

Last edited by zhanghao; 11-07-2015 at 06:39 PM.
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