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• Fwd: Normalizing For Number Of Tags
  Hi Nadege, I am forwarding your question to galaxy-user@bx.psu.edu which is the best place to sen...
• Do I need to normalize the ChIP-seq BAM files before run MACS?
  Hi Everyone, The experimental ChIP-seq datasets I am analysing have two times of aligned reads t...
• Analysis of forward and reverse reads
  Hello. Newbie here: I have recently done some chip-seq, and for each sample, I have different ...
• rmdup - remove PCR duplicates from ChIP-seq data
  I have aligned my chip-seq data with bow tie and wanted to remove PCR duplicates. I ran rmdup in ...
• HELP with FastQC Webpage
  Hello, I have created a workflow for ChIP-Seq, yesterday everything worked fine and I was able t...
• 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...
• Finding Percent Totals in RNA-Seq
  Does anyone know how to sum and divide RNA-Seq datasets? I have two datasets (FPKM values) and wa...
• Macs2callpeaks bedgraph/ucsd genome browser
  Hello, I am relatively new to Chip-seq analysis and have a question regarding macs2callpeaks. O...
• Annotating ChIP seq peaks in Galaxy
  I'm analyzing ChIP seq data using Bowtie and then MACS with the Galaxy web instance, and now want...
• Batch workflow with two different inputs each time?
  Dear Galaxy Community, I have actually installed Galaxy on our cluster, and I am now trying to d...
• (No Subject)
  I am new to Galaxy and am using it for analysis of BLAST results and phylogeny. I have uploaded a...
• How to know if mapping to reference genome was succesful?
  Given a set of BAM files for single-end reads just mapped with BWA tool, how can I have an overvi...
• 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...
• Normalization on Single End and Paired End reads
  Hi there. I want to assemble a transcriptome with Trinity using reads that are both paired- and ...
• Column Join Feature
  Hi, I am analysing some RNA-seq data and have two different datasets, total RNA plus enzyme and ...
• mapping RNA-seq reads with "N" in the middle of each read
  Hi all, I am performing differential gene expression analysis using the Tophat-Cuffdiff protocol...
• Counting Rna-Seq Reads Per Class.
  Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cuffli...
• Window And Merge Workflow?
  Hi, I have two datasets, both from the same cell type and same genome build. One data set is ch...
• SICER Failed to
  I have been trying to run SICER on my ChIP-seq data set. Seequnces were aligned with bowtie2, seq...
• 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...
• Chip Seq analysis with multiple biological replicates for differential expression
  Hello, I am very new to sequence data analysis and had some structural questions. I am trying to ...
• CuffDiff and normalization between runs
  Dear All! I am currently conducting an RNA-Seq experiment in which i have several samples (1 nor...
• 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...