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• HELP! My HT seq table counts are in zero
  Hello!! I am running HT seq using my sam files (obtained from bowtie) and the gtf file I obtaine...
• Clustering With Cuffcompare Or Cuffdiff Results
  Dear Sir or Madam, I am planning to do clustering of several libraries based on the output of cu...
• DEXseq count reads tool obtaining only zero counts for all exons
  I'd like to run DEXseq on my RNA-seq dataset to identify any potential differences in exon inclus...
• RNA-seq analysis in Galaxy
  I am doing RNA-seq analysis for several mouse samples and I encounter problems during differentia...
• Alignment rate differes using hg19 and hg38
  I have some RNA-seq fastq files.I'm using HiSat to align the fastq files. To do so, I use the bui...
• RNA-seq data to check impact of PCR duplicates
  I have aligned my reads using HISAT, filtered and merged my data into a BAM file. I have tried re...
• Are reads number normalized on transcript length ?
  Hello, I used featurecounts to obtain reads number from a RNA-seq file (.bam). I would know if t...
• Cuffdiff Errors: "Loading reference annotation" and "Inspecting maps and determining fragment length distributions". whats that mean?
  Hello everybody, I'm very new in RNA seq analysis I have run cuffdiff on 3 condition dataset coll...
• Duplicate row names error with EdgeR on FeatureCounts files
  Hi all, I created tabular count files using FeatureCounts with a GTF file (iGenomes, UCSC hg38) ...
• Bowtie Seed Length (-L) And Non-Unique Reads Mode (M=-1)
  Hi there, I have two questions regarding alignment using Bowtie: 1. Is there a way to set the S...
• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• 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...
• Poor overall alignment rates
  I am having problems with the alignment process for some data that I obtained through NCBI GEO da...
• 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: Matched on error
  Hello, I am doing my first RNA seq data analysis using galaxy. I have assembled my transcripts u...
• This job was terminated because it used more memory than it was allocated
  Hello, I have always encountered such problem "This job was terminated because it used more memo...
• How to identify the SiRNA abundance from transcriptome data
  Hi all, I am having transcriptome data of c.elegans i would like to analyse the differential exp...
• "View Details" Of Tophat Alignment
  Hi All, After I finshed Tophat alignment for RNA-seq, I took look at the details of parameters b...
• count and compare microRNA expression value in RNA-Seq data on Galaxy
  Hello, I have a question, I want to count and compare specific microRNA expression value in BAM ...
• htseq read counts zero
  Hi, I have imported some fastq files (homo sapiens) from http://www.ebi.ac.uk/ena/data/ to Galax...
• Filtering BAM files from HISAT2
  Hi. I am new to rna-seq and I have a couple of quick questions. My input was paired-end non-stran...
• Single cell RNA seq data set alignment
  Hello, I have a single cell RNA seq data (600 cells) and I would like to see the possibility to...
• Cuffdiff fragment length and SD
  Hello, I am new at using Cufflinks. I was wondering if someone could help me figure what "Avera...
• RNA-Seq raw count data analysis using GALAXY
  Hi, I have downloaded the raw_readcounts files (.txt files) from an RNA-Seq experiment using GSE ...