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Question: TopHat for Illumina or TopHat2 for Illumina data - what's the difference?
1
gravatar for m.maleszewska
4.5 years ago by
m.maleszewska • 20
Netherlands
m.maleszewska • 20 wrote:

Hello,

I wonder if I should use TopHat for Illumina or TopHat2 to align data that come from Illumina? Is there a difference? Or is TopHat2 simply a newer version and I should use that?

All best,

Monika
rna-seq tophat alignment • 3.2k views
ADD COMMENT • link •
modified 4.5 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.5 years ago by m.maleszewska • 20
0
gravatar for Jennifer Hillman Jackson
4.5 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Tophat2 is the newer version of the tool from the tool authors with added features. A new Galaxy wrapper was created to support these features. The changes can be reviewed here: http://tophat.cbcb.umd.edu/index.shtml

Best, Jen, Galaxy team
ADD COMMENT • link written 4.5 years ago by Jennifer Hillman Jackson ♦ 25k

Hi Jen, I use Galaxy regularly, and used TopHat2 earlier without any problem. However, just a day ago,  when I was trying to align 'fastq groomed' files with TopHat2, I was getting an error (after a long run): "The Cluster DRM System has terminated this Job". I learnt it's something to do with the limits (time and memory for a run) set by the Galaxy admin? All my 15 'fastq groomed' files eventually returned with the same error message: "The Cluster DRM System has terminated this Job". As I said, I never had problems earlier with aligning my 'fastq groomed' files with TopHat2.

 Our Galaxy runs on Helix clusters. Please advise me. Thanks in advance.

ADD REPLY • link modified 3.7 years ago • written 3.7 years ago by lax • 0

Hello, If the jobs are running out of memory or exceeding wall-time limits when using the new version of the tool, the administrator of your Galaxy can adjust these usage quotas (limits). I suggest contacting them with your examples and asking. Thanks, Jen, Galaxy team

ADD REPLY • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
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