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• Problem with merge collection
  Hi, I am analyzing the RNA-seq data on Galaxy. I am facing an issue with Merge collections tool....
• Merging BAM files: bamtools not found
  I have BAM files from aligning paired end Illumina reads. I would like to merge the aligned seque...
• How Should I Include Biological Replicates In Cufflink/Cuffdiff?
  Dear team, I have a few questions regarding RNA-seq data analysis. I want to compare transcripto...
• Fwd: Tools: Merge Regions Of A Single Query
  Date: September 27, 2006 5:58:47 PM EDT To: galaxy-user@bx.psu.edu Subject: tools: merge regions...
• Merge BAM files
  The Merge BAM files option is no longer available on NGS:Sam Tools. Where has it gone? How can I ...
• Cuffdiff
  Dear All I have simple and question for cuffdiff should we run cuffdif on merge transcript file (...
• Duplicate Row Removal in Merged FeatureCounts
  Hello,   I am trying to transfer merged featurecount data into an R-studio package called RNASe...
• Parameters For Merging Bam Files
  Hi All, I want to merge the Tophat output (Accepted Hits) of Several datasets. I want the merged...
• Merging Of Illumina Paired End Files
  I have 3 illumina paired end reads of exome capture of the sample. I want to assemble these reads...
• htseq-count error with strand data
  Hi! I am running htseq-count for a RNA-seq and I got this error: Fatal error: Unknown error occ...
• Making paired-end reads the same length
  I have paired-end data (in two separate files).  I have groomed my files, and would like to filte...
• How to use cuffmerge and cuffdiff
  I am trying use Galaxy to analysis the yeast RNA-seq data. When I want to try the cuffmerge and c...
• Can someone give me a foolproof instruction on how to merge R1 and R2 illumina fastq files
  Dear Galaxy experts,               I need to merge R1 and R2 Illumina paired end reads. T...
• Merge Bam files
  I am trying to merge 3 .bam files (different alignments of the same ChIP-seq run), one has 5.9M r...
• Freebayes issue on merged data
  Hi, I am completely new to this field so I'm hoping this is a simple mistake on my part. I'm tr...
• 3' Adapter Trimming Using Fastx-Toolkit Clipper
  Hi all, I am analyzing miRNA sequencing now. My data is 51bp, single -ended and ~5 M reads. I wan...
• Biological Replicates on galaxy/ DeSeq analysis
  Hi, I am doing RNA seq analysis and I want to preform Deseq. I have 2 replicates for each condit...
• 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...
• Multi-join name of the dataset
  Hi, I am analyzing RNA-seq data on multiple fastq files. I processed all of them to get the Feat...
• Tutorial Help: Only see one row of data
  When I was doing the tutorial and it told me to sort 5 data points, I know I should see at least ...
• Files queued in cufflinks for 4-5 days
  Hello I am quite novice but have loved using Galaxy for RNAseq - Ive had sample queued for cuffl...
• Merging Multiple Unaligned Bam files
  Hi everyone, I am developing a workflow in Galaxy for Variant Analysis and have hit yet another ...
• Merge RNA-Seq files in CLC Genomics Workbench ?
  Hi I now analyzing my RNA-Seq data (illumina, 50bp paired end) using CLC Genomics Workbench to ve...