TopHat2: --read-realign-edit-dist = 0 or default options?

Question

[noeD]

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

[Carlo Yague]

You shouldn't use tophat for a new project as it is deprecated. Use HISAT2 instead or alternative aligners like STAR or BBMAP.

[noeD]

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!

[Carlo Yague]

The authors of TopHat have moved on to a new project last year called HISAT2, which does the same job as TopHat but better.

"Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way." source

[noeD]

Thank you for your help!