TopHat2: --read-realign-edit-dist = 0 or default options?
Hello :)
I have RNA-seq data from human samples and I am looking for a RNA-seq aligner. I have read some papers and I think that I will use TopHat2. I am wondering if it is better using --read-realign-edit-dist = 0 in order to map the read in all mapping steps or to use the default options.
Do you have any suggestions?
Thank you in advance
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You shouldn't use tophat for a new project as it is deprecated. Use HISAT2 instead or alternative aligners like STAR or BBMAP.
Thank you for your reply and suggestions. Why is it deprecated? In what? I have read TopHat2 's paper that it had better performance that STAR... Thank you in advance!
The authors of TopHat have moved on to a new project last year called HISAT2, which does the same job as TopHat but better.
Thank you for your help!