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Question: why TopHat doesn't read my compressed dataset collection (Fastqsanger.gz)? -- Deprecated tool, use HISAT2 instead
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gravatar for Fat.eldefrawy
7 months ago by
Fat.eldefrawy • 10
USA
Fat.eldefrawy • 10 wrote:

Hello everyone, I'm very new in RNA seq analysis, I'm trying to align my paired-end dataset collection ( fastqsanger.gz format) by Tophat on galaxy, but unfortunately, it shows me no fastqsanger dataset collection available. Does that mean I need to uncompress the dataset and rearrange it on collections again? An additional question is any way to make an edition ion dataset collection like rebuilding, add replicate, etc? Any suggestion will be appreciated

tophat fastqsangergz galaxy collection hisat2 • 341 views
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modified 7 months ago • written 7 months ago by Fat.eldefrawy • 10
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gravatar for Jennifer Hillman Jackson
7 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

Tophat is a deprecated tool and was never updated to accept input data in fastqsanger.gz format. If you really need to use this tool, the data must be in uncompressed fastqsanger format.

I would suggest using HISAT2 instead, even if this was not a problem. This tool accepts fastqsanger.gz inputs, individual datasets or collections. For help in understanding the usage, and the options that need to be set to report alignments for downstream tools (Stringtie, Cufflinks), please see the Galaxy Tutorials: https://galaxyproject.org/learn/

Specifically, this tutorial covers HISAT2 and other current RNA-seq tools/methods and will run at https://usegalaxy.org:

Thanks! Jen, Galaxy team
ADD COMMENT • link written 7 months ago by Jennifer Hillman Jackson ♦ 25k
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gravatar for Fat.eldefrawy
7 months ago by
Fat.eldefrawy • 10
USA
Fat.eldefrawy • 10 wrote:

Thank you, Jennifer. your suggestions helped me more
ADD COMMENT • link written 7 months ago by Fat.eldefrawy • 10
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