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  I am involved in an RNAseq project in which mutliple tissues of an organism are being analysed. N...
• 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 ...
• Combining Reads from 2 Lanes
  Hi, I'm running an RNA-seq analysis to look for differentially expressed genes. I'm using sing-e...
• 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...
• Merge Bam files
  I am trying to merge 3 .bam files (different alignments of the same ChIP-seq run), one has 5.9M r...
• Galaxy For Gene Expression Comparison
  Hello, I am comparing RNA expression in two groups of rats, a drug treated group against a cont...
• Cuffdiff-differential gene expression-NOTEST
  Hi I am just starting up and getting to know and analyze my data from the RNA-seq. I have 2 biol...
• Cuffdiff: selecting replicates in a different order gives me different numbers of differentially expressed genes. Why?
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• samtool sort error in sorting BAM files by read name
  Hi, I'm trying to sort my BAM file by read names (-n) on Galaxy but it gives me this error: [bam...
• Need help with "Merge BAM Files" tool
  Can I merge more than two BAM files together at once? I have three Bam files that I need to merge...
• Query for inputting Hisat2 BAM with dataset collections for Stringtie analysis
  Hi, I have data set collections ( 3 biological replicates) that I could run on HiSAT2 and I have...
• How can I merge two single-end mapping data
  Hi, I am analysing my ChIP-Seq data which generated by paired-end sequencing. But due to some ex...
• Slice Bam
  hello all, Does anyone know if in order to use Slice bam I need to sort the bam file first or do...
• Cuffdiff Biological Replicates
  Hi guys, a bit of confusion about how to give cuffdiff certain outputs: having 1 control and 8 tu...
• HT-seq counts help
  Hi everyone, I need to analyse .bam files (sorted and indexed) that have been mapped by someone ...
• Using DiffBind in Galaxy to generate PCAs of ChIP data
  Hi all, I'm trying to use DiffBind in Galaxy to make a PCA or multiple ChIP-seq sets. I have the ...
• How to use Deseq2 to merge the biological triplicates (for two seperate conditions) for analysing differential expression of genes
  I am very new to R, I have used Deseq2 package after my feature counts. I have 2 stages of contro...
• Incorporating biological replicates to identify statistically significant changes between two different "treatment" samples and one "control" in ChIP-Seq
  I performed a ChIP-seq experiment in which I'm looking at H3K4me3 levels under three conditions. ...