Question: Problem with running TopHat2
gravatar for ntt28
4.4 years ago by
United States
ntt280 wrote:


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.




rna-seq • 945 views
ADD COMMENTlink modified 4.4 years ago by Jennifer Hillman Jackson25k • written 4.4 years ago by ntt280
gravatar for Jennifer Hillman Jackson
4.4 years ago by
United States
Jennifer Hillman Jackson25k wrote:


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:

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 COMMENTlink modified 4.4 years ago • written 4.4 years ago by Jennifer Hillman Jackson25k
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