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• Content of the built-in hg38 genome annotation available in Featurecounts
  Hello, After executing featureCounts on my BAM file using a built-in genome (hg38) from Galaxy ...
• Read Length Distribution
  Hi, Is there a tool or easy way to obtain a read length distribution on a set of 454 reads in fa...
• Error using stringtie - AttributeError: 'NoneType' object has no attribute"
  Hi, I have **RNA-seq data** and I am interested in whole gene expression results but also transcr...
• Error while running cuffdiff "Fatal error: Exit Code 1()"
  Hello, I recently posted about having problems with cuffdiff (https://biostar.usegalaxy.org/p/18...
• Occurence of reads
  Hi, I already obtained the sequences with the right length. But now I would like to know how oft...
• Cuffdiff 2.2.1.5 error with cummeRbund SQlite. "Fatal error: Exit code 1 () -- use version 2.2.1.3 instead
  Hi, so as a disclaimer, I am very new to RNA seq analysis. I received the following error while r...
• Alternative To Fpkm From Cufflinks
  Hi all, Is there any way to find out the number of reads aligning to a transcript rather than the...
• Chip-Seq Normalization To Total Number Of Reads
  Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datase...
• How do I get +/- strand orientation info from my RNAseq run?
  I made a RNAseq library using a stranded-RNAseq-library prep kit. The kit only amplifies the tran...
• Cuffdiff fragment length and SD
  Hello, I am new at using Cufflinks. I was wondering if someone could help me figure what "Avera...
• Finding exogenous transcripts in RNA-Seq bam files
  Hello, What is the easiest way to find and count reads for exogenous transcripts (Cre, GFP, etc....
• Read length from HT-Seq
  Hi, Sorry for asking this very basic question. I have paired-end RNA-Seq data. After initial ada...
• Unable to select GTF file from history in featureCounts (Galaxy version 1.6.0.3)
  Hello, I have recently begun mapping Drosophila RNA-Seq data with STAR (in Galaxy), and I am now...
• Cuffdiff Fatal error: Exit code 1 () Error: number of labels must match number of conditions number of labels must match number of conditions
  Hi! I ran into a problem using Cuffdiff. (I am using a local version of galaxy). When I try to ...
• RNA-Seq analysis for 2 genes
  Hi, I did RNA-seq for 20 samples and I am interested in the differential expression of normal tra...
• Error - Heatmap generation / visualization from RNA-seq data using DESeq2 workflow
  Hi I wanted to try generating heatmaps of gene expression using normalized counts file obtained ...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• Error with cuffdiff
  Hi, I'm new to Galaxy and the tuxedo pipeline but have managed to get my data to the point where...
• Cuffdiff not working in Galaxy
  Hi, I'm trying to run cuffdiff as part of an RNA-seq project, and it's not working. I've tried l...
• CuffDiff error on Local Galaxy
  HI, I am running local instance of Galaxy on my linux mint system. When I try to run CuffDiff, ...
• Cuffdiff Changes
  Hi, I am wondering why Cuffdiff suddenly gives many more significant DE genes? I have used same ...