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Posts by jevanveen
... TopHat has been largely replaced by newer algorithms. Is there a reason you must use TopHat? If not, it's better to proceed with a pipeline using Hisat2 or Star for alignment dependent fragment counting or Kallisto or Salmon for alignment independent fragment counting. I've used Star followed by DEs ...
... Hello! Has anyone had success pulling data from Salmon into MultiQC? It doesn't appear as an option in the version of MultiQC on the main Galaxy instance but maybe someone has done this with the "custom input" parameter? If not, perhaps the version of MultiQC on the main Galaxy instance can be u ...
Answer: A: salmon gene quant to DESeq2
... i had the same issue and resolved it as follows: inputs: salmon quantification (not gene quant) files generated in Galaxy salmon transcript to gene map - tab delimited text file from ensembl when i run as is, i get the line2/6elements error. the fix was simple - i removed header line from the ta ...
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