TopHat2 Download URL Broken?

Question

[stoptime_armstrong]

$ wget https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz

--2021-11-24 18:44:24--  https://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
Resolving ccb.jhu.edu (ccb.jhu.edu)... 128.220.233.141
Connecting to ccb.jhu.edu (ccb.jhu.edu)|128.220.233.141|:443... connected.
OpenSSL: error:1414D172:SSL routines:tls12_check_peer_sigalg:wrong signature type
Unable to establish SSL connection.

Also their other download links seem to be broken?

https://ccb.jhu.edu/software/tophat/downloads/

Is there a mirror for TopHat2?

[lieven.sterck]

any particular reason you (still) want to download/use TopHat(2) ?

here is an extract from their website:

Please note that TopHat has entered a low maintenance, low support stage as it is now largely superseded by HISAT2 which provides the same core functionality (i.e. spliced alignment of RNA-Seq reads), in a more accurate and much more efficient way.

Last update is ~6 years old

[Charles Warden]

I am more likely to use STAR on new samples, but I think TopHat2 can sometimes be useful (and I think I might prefer it over HISAT2).

I have collected some notes here:

http://cdwscience.blogspot.com/2019/01/tophat-really-isnt-that-bad.html

[lieven.sterck]

True, I personally also prefer STAR over HISAT2 (and even TopHat2),

[Charles Warden]

Yes - I was saying that I am more likely to use STAR than TopHat2 on new samples, although you can get some sense of how much of a difference that makes in the link below (which is indirectly linked from the first link):

https://sourceforge.net/projects/rnaseq-deg-methodlimit/files/Target_Recovery_Status.xlsx/download (Target_Recovery_Status.xlsx file)

I am not sure if we are already on the same page, but I was saying that I actually prefer TopHat2 over HISAT2 (in addition to preferring STAR over HISAT2). Part of that relates to the extra files produced by TopHat2, and that is admittedly not captured in the statistics in the file above (since I was trying to emphasize the differential expression methods more so than the aligners). That said, one of the main goals was to try and quantify my experience that you can't lock down all of the methods in advance, which is part of what I mean when I say TopHat2 can still have value today (even if you might first use a STAR alignment for most samples).

Eventually, I might add the HISAT2 alignments for comparison in the linked Excel file, but I don't think that will be in the immediate future.

Answer 1

[GenoMax]

I randomly clicked two three links from downloads page you linked above and they all appear to be working. wget also worked with the link above. So definitely a local problem for you.