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• How to get raw reads from bam file
  Hi, I can't figure out how to get raw reads counts from a bam file. I have 3 different experimen...
• How to extract the 16S sequences from your illumina data?
  I would like know the steps in usegalaxy.org for extract my sequences in raw from Illumina for ob...
• No ht-seq in main Galaxy menu?
  Why is there no way in the main Galaxy menu to produce a raw counts matrix (not normalized and no...
• What to do with Cuffquant .cxb files
  I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a ref...
• Can limma's voom take normalized counts as input?
  Hi,      I am currently analyzing some RNASeq data from TCGA - which is data that has been proce...
• voom normalized count data matrix (Differential count 0.3.0)
  Hi, I have used voom from the "Differential count" package and it worked smoothly. I would like t...
• Raw Counts From Galaxy
  Dear all, I would like to analyse some RNA-Seq I obtained in the chicken. I am implemented the...
• 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 ...
• htseq-count no read align
  Hi I am trying to get raw count of mapped read, so I am running htseq-count on tophat accepted h...
• Using DESeq w/ counts from different RNASeq experiments
  Hello there I have count files from 3 different sequencing experiments on similar samples but wi...
• Bowtie Raw Input
  Hi There Im trying to map RNA-seq data to a reference genome in Galaxy (Main instance) using bot...
• Extracting the read counts from a collapsed fasta file?
  I have collapsed my fastq file so I know have the output fasta file which contains all the unique...
• Read count across interval
  Hello, I'm trying to retrieve a score for ATAC-seq (similar processing to ChiP-seq data), at an i...
• DESEQ2 is not normalizing HTSEQ counts for some samples
  I have RNAseq HTSEQ count data for 3 individuals collected at 3 time points. I would like to perf...
• Galaxy app to retrieve selected raw reads
  There are many previous threads regarding how to retrieve selected raw reads from fastq files off...
• Normalization of RNA-seq data
  Hi, I am wanting to normalize my RNA-seq data without running a differential gene expression on...
• how to perform alignment using Hisat2
  Actually I have several questions to ask but I try to be very much to the point. I want to uploa...