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Question: TopHat for illumina
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gravatar for sergio.gma91
2.6 years ago by
sergio.gma91 • 0
USA
sergio.gma91 • 0 wrote:

Hello,

Any idea when the TopHat for illumina tool will come back?

Thanks.

Greetings,

Sergio
rna-seq • 794 views
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modified 2.6 years ago by Martin Čech ♦♦ 4.9k • written 2.6 years ago by sergio.gma91 • 0

This tool may be deprecated (meaning, hidden for use in older workflows, but not available for new analysis in the Tool Panel). Use Tophat (2) instead. Our team will write back with confirmation.

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k

TopHat (2) is also not present in the tool panel, can I use only TopHat?

Greetings,

Sergio

ADD REPLY • link written 2.6 years ago by sergio.gma91 • 0

Yes, the name is Tophat. The (2 or 2.x) was to indicate the version of the tool, sorry if that was confusing. (Tophat for Illumina was version 1.x)

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for Martin Čech
2.6 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

Tophat is hidden as it is outdated. You can rerun old tophat jobs for the reproducibility purposes but for new jobs please use the superior version Tophat2. Given the naming issues in between first and second versions of the same software we decided to name the tool just Tophat in the Galaxy interface.

You can reach it directly on Main by visiting this link: https://usegalaxy.org/root?tool_id=toolshed.g2.bx.psu.edu/repos/devteam/tophat2/tophat2/0.9

You can also check Options/Requirements in the tool form menu to check the exact version of SW that is being used.
ADD COMMENT • link modified 2.6 years ago • written 2.6 years ago by Martin Čech ♦♦ 4.9k
0
gravatar for sergio.gma91
2.6 years ago by
sergio.gma91 • 0
USA
sergio.gma91 • 0 wrote:

Is it HISAT the newer version of TopHat2?

Sergio
ADD COMMENT • link written 2.6 years ago by sergio.gma91 • 0

No, this is a different tool but is based on some common underlying software. You can try using both and comparing to see which produces better results for your project.

ADD REPLY • link written 2.6 years ago by Jennifer Hillman Jackson ♦ 25k
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