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• sequence information for mRNA transcripts
  Hello, Is there any way to retrieve mRNA sequence in FASTA format for all the novel transcript g...
• Error in Cuffdiff analysis with reference genome build
  Hello All, I am using cuffdiff for my differential gene expression analysis. I am doing three co...
• Cuffdiff-output-couldnot find fasta record for a scaffold
  Dear Galaxy team When i ran cuffdiff for my merged transcripts file using a custom reference gen...
• assembled transcripts TO BLAST2GO
  Hi , i want to compare the ontologies of genes generated from cuffdiff output and use it for BLA...
• Solution For: Error Running Cuffdiff. Error: Cannot Open Reference Gtf File Condition, Control For Reading
  Hi, I ran into this error running cuffdiff. I had a hard time debugging this user error, so I th...
• Fwd: Cuffdiff Using The Combined Gtf Files From Cuffcompare
• Differential Expression in bacteria RNA-seq
  Hello, I got a problem in Cufflinks: I need to analyze fastq file from a RNA-seq (I got bacteria...
• create sqlite from cuffdiff terminal
  if there is a way to put an option when you run cuffdiff from terminal so that you can get an sql...
• makeblastdb error, but not when run from commandline
  Hi, I'm trying to create at blastDB and get errors. When I run the command that Galaxy uses at t...
• q values p values from Cuffdiff are same for different samples
  I ran some human samples for mapping with BWA, Cufflinks, and Cuffdiff. When I looked at signific...
• blast2go ontologies comparison
  Hi, i posted this question earlier also but received no feedback, kindly help.   I want to com...
• No output from Cuffdiff
  Hi, I've been running Cuffdiff on Galaxy today, exactly as I did last week (using the same refer...
• CummeRbund input from Cuffdiff output
  Hello All I just finished my Cuffdiff on a set of practice data, and I am planning to visualize...
• Issues with Using CuffDiff Tool in Galaxy
  Hi,   I am analyzing microRNASeq data. My pipeline is qc reads, bowtie for alignment, cufflinks...
• cuffdiff tabular file conversion
  Hello, I just finished running differential expression analysis using cuffdiff. The end result i...
• FASTA consensus from BWA-MEM mapped MinION data?
  Does anyone know how I can I generate a FASTA consensus from BWA-MEM MinION data using Galaxy?
• extract fasta file from Galaxy
  I am trying to extract fasta file from galaxy after cuffcompare analysis which gave me combined t...
• New Fasta Sequence From Variant Calls File
  Hi, Is there a way in Galaxy to create a new FASTA reference sequence from a reference sequence ...
• fasta sequence from differential expressed gene
  Hi, I am Galaxy user. How could I get fasta sequences of differential expressed genes from Galaxy...
• Tarcking ID in cuffnorm output and TestID (geneID) in cuffdiff output, are they the same?
  Dear all, I found in the output of cuffnorm there was no locus information corresponding to my d...