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Question: Problem with running TopHat2
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gravatar for ntt28
4.4 years ago by
ntt28 • 0
United States
ntt28 • 0 wrote:

Hi

I am running the TopHat2 on Galaxy, i already uploaded the data on my history but whenever i run the TopHat2, the web-based always told me that the files in my history are not supported by TopHat2. However, my files are in "fastaq" and i think this is the right format..Hence, please kindly to let me know what i can do now? are there any files that TopHat 2 is supporting to.

Thanks

Best

Nu
rna-seq • 945 views
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by ntt28 • 0
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gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

The format needs to be in ".fastqsanger". This wiki can explain how to determine what type of fastq data you have, if any quality score rescaling is needed, and how to reassign the datatype as needed. 

Review this section and especially the following about FASTQ specifically. Correct datatype labels are important, but the underlying data must be a match in content for your analysis to come out with the correct answers:
https://wiki.galaxyproject.org/Support#Tool_doesn.27t_recognize_dataset

BTW - this may have been a typo - but ".fastaq" is not a Galaxy datatype - I suspect that you meant to type ".fastq". If you happen to have ".fasta", you can still use Tophat2 with default quality scores. Use the tool "Combine FASTA and QUAL" to do this. Use default options and only provide the ".fasta" file as input.

Take care, Jen, Galaxy team
ADD COMMENT • link modified 4.4 years ago • written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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