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• sort reads by start position
  I did RNA sequencing and many reads map to tRNA regions. Specific tRNAs are completely covered b...
• RNA genes count using HTseq
  Hello: I am new to Galaxy, but based on my understanding of how things work, I mapped some RNA-s...
• Visualizing RNA STAR Bam file
  hi I'm working through the RNA-seq tutorial using the Pasilla knock down example. I have made i...
• IGV read color question
  What do the colors correspond to on IGV? Most of my reads are red with very few gray and blue col...
• Finding Open Reading Frames And Corresponding Genes
  Hi I am sequencing a bacterial genome and have assembled my Illumina reads (40 bp single) using b...
• rna seq read cleaning
  Please suggest me a tool for removing bacterial contamination from RNA seq reads before assembly.
• Cuffmerge Question
  I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find...
• Only First 5000 Reads Are Displayed In This Tile
  Hi During the visualization of my mRNAseq data, some area have red line indicating that only the...
• Extract fastq sequences from BAM with flag Supplementary alignment
  Dear all, after running BWA-MEM on a fastq dataset, I identified some "supplementary alignment" r...
• read representation using trinity
  Is there any way to analyse the trinity assembly for RNA seq read representation and Transcriptom...
• 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...
• Rna-Dna Converter In Fasta Format
  Hi all, I want to to map my sequencing reads to miRNA reference database . Anyone know how to con...
• Any tools for separate unpaired reads in paired-end sequencing fastq files?
  Hi, I would like to know if there is any tool can do the following job? I have some data files ...
• Cufflinks assembles very small number of transcripts from RNA-seq data
  I mapped RNA-seq data to reference genome and tried to assemble transcripts using cufflinks.It is...
• 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...
• Duplicate Reads
  Dear all, When is it necessary to remove duplicate reads from your RNA Seq analysis? Is it requi...
• Can anyone share a workflow of differential gene expression on multiple conditions (>3) and triplicates?
  Hey guys, I just started using Tophat-cufflink on Galaxy today. But the example I found was quit...
• Reference genome of Arctica islandica
  Hello, I work on mitochondrial genome of Bivalvia. I would like to align reads generated by NGS ...
• How do I convert numerals to nucleotides for RNA-Seq mapping?
  The FASTQ reads I imported from EBI SRA (SRR064843) appear to be numeric (0-3) rather than AGCT....