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• Analyzing Rna-Seq Replicates Using Cuff(Links/Compare/Diff)
  Hello! I have 10 human RNA-Seq samples consisting of 3 groups (2 replicates per ...
• 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...
• comparisson of RNA-seq FPKMs across samples
  Dear BioStars community, I am trying to "recycle" some RNA-seq data published as supplementary m...
• normalisation between different ChIP-seq data
  Hi there, I guess it is a recurrent problem, but I haven't found a satisfying answer yet. I have ...
• Why Don'T We Get Fpkms From This Gene?
  Hello, We are using BAM to map Illumina reads to a bacterial genome, followed by Cufflinks o ge...
• Tool problems when using older versions of downsampled tutorial data
  Hi, I'm a newbie in Ref-seq and I'm trying to make a pipeline using HiSat -> HtSeq -> DESeq...
• 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...
• Cuffdiff Tracking File Does Not Report All Genes And Trancrips From Reference Annotation?
  Hi, Galaxy user. I ran into a problem when using Cuffdiff 1.2.1 in Galaxy local instance to check...
• Questions On Cuffdiff Output And Browser Visualization
  I would really appreciate someone's input on some issues I am having with my cuffdiff output for ...
• I am slightly confused about the input requirements for the differential expression tool - last step of Trinity
  Hello all, I have a pressing question... To start with, I have read the Trinity methods paper ...
• Cuffdiff output redundant genes
  Hello, I am using the Galaxy tool Cuffdiff to analyze the RNA-seq data. But for the output file "...
• Galaxy Tuxedo Protocol Questions
  Hi everybody, I'm totally new to RNA-seq analyses and it's my first time doing this and using Ga...
• Any Thing Wrong With My Cufflink Process In Galaxy?
  Dear all: Recently, I run cufflink in galaxy on the internet. I want to compare two samples, How...
• Cuffconfusion
  ok, im really confused now about cufflinks and its tools. All I wanted was to look for different...
• salmon output files in Galaxy
  Hi all, I used Salmon tool in Galaxy to both align to my de novo transcriptome assembly and to qu...
• Intersect more than two vcf files
  Hi everyone, I have nine vcf files that I'd like to intersect. I want to know which, if any, gen...
• Variant calling with 5x coverage, human genome
  I am new to analysing raw sequencing data - apologies in advance if I seem not to understand what...
• MD Plot with Glimma starting from DESeq2 results
  Hi, I'm trying to visualize results from the DESeq2 pepeline in interactive html, useing Glimma....