TopHat and HISAT2
Hey, all. Why TopHat gives totally different alignments when I change the Library Type (First strand vs. Second strand) and for HISAT2 the alignments are pretty much the same (Reverse vs. Forward). I am trying to read the papers that describes them but so far, couldn't explain this.
I am aware of the fact that TopHat is an outdated tool but I am trying to understand the process. Is someone here that has an idea why this might happen? Thanks.
Additional Info: I am using Galaxy, other than the Library Type, I left the default option. I tried to upload a print screen from IGV but it wouldn't work.
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Hello Sammy!
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