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• Cufflinks Fpkm
  Hi: I gain the SOLiD sequencing data.I used bowtie to map human genome then I sort the s...
• zero fpkm value in cufflink
  hi i have done cufflink on my sra seq according to the ngs pipeline. the result says fpkm value...
• All fpkm values are 0 (zeros)
  I'm trying to establish a rna-seq workflow to analyse a bacterial transcriptomics, however, when ...
• How To Extrapolate Differentially Expressed Genes After Running Cuffdiff?
  Hi guys, have a question about the cuffdiff output "differential expression testing". For most o...
• cuffdiff-quartile normalization method
  Hello Why does the quartile normalization method does not produce any FPKM values for my data wi...
• Comparing FPKM Values Between 2 Cufflinks Outputs
  Hello, apologies if this is a dumb question, I am relatively new to RNAseq. I have processed 9 sa...
• zero cuffdiff FPKM values SusScrofa
  Good morning, I am a beginner in RNAseq Galaxy interface and I have a problem with all zero FPKM...
• rRNA FPKM values all are zero
  Hi, I have used Tophat2 and cuffdiff to analyze the S.cerevisiae RNA-seq data. But the rRNA FPKM ...
• stringtie output from multiple samples into an FPKM matrix
  Hi all, Anyone have a good set of steps to take the stringtie transcript-level expression output...
• Counts vs FPKM
  I was able to retrieve the counts from my RNAseq analysis via Cuffdiff so as to compare with the ...
• Cufflinks analysis remains in que without running
  Hi Team, Loving Galaxy! When I run my data, I use the same protocol for most all datasets. Howev...
• Cuffdiff Values Different For Same Sample
  Hello forum, I have ran cuffdiff with two samples, treated vs untreated, and had certain values a...
• Is this correct way ??
  Dear Sir, while doing RNA-Seq analysis, after mapping, i have downloaded mouse reference gene se...
• deepTools computeMatrix sorted values WITH gene identifiers
  I've performed a computeMatrix analysis on a ChIP-seq sample referenced to gene TSSs. This genera...
• Inconsistent Cuffdiff Output-Corrected Question
  Dear all, I have two samples, treated and untreated. I ran cufflinks and had the following FPKM: ...
• fold change calculation for RNAseq data
  Hi Everybody, I would like to analyse the fold change of RNAseq data. What is the best option to ...
• The giant different FPKM value of same gene between cufflink and cuffdiff.
  It differs a lot (10 times as large) between cufflink outputs "gene_FPKM tracking" and cuffdiff o...
• How to get counts for transcripts for all replicates
  Hi BIOSTARS, I have lots of samples that have been aligned to mm10 using RNA STAR. I have succes...