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• Alignment of entire bacterial genomes
  How entire genomic alignment of bacterial species can be carried out????? I have added ten genom...
• Galaxy for alignment for genomes of bacterial species
  Galaxy can be used for alignment for genomes of bacterial species or not?? How genome sequence ca...
• Genome of Campylobacter jejuni 81-176
  I am doing RNAseq analysis and i am at Tophat step. My bacterial strain is Campylobacter jejuni 8...
• RNAseq analysis for Bacterial genomes
  Hello, I am interested in using the tuxedo suit to analyze RNAseq data from the bacteria Strepto...
• Need help with "Map with Bowtie for Illumina" tool
  Hi, I mapped my illumina sequences with one reference bacterial genome and got bam file. Does any...
• Bacterial Sequence for Variant Analysis
  I am analyzing paired-end data for bacterial genome and have done the following steps: *FAST...
• Use whole genome or cDNA sequences for RNAseq alignment
  Hello,    I'm working on my first RNAseq analysis, and I'm unsure of how to proceed with my TopH...
• Bacterial Metatranscriptomes
  Hi everybody, I am trying to perform metatranscriptomic analysis on gut samples. Whereas the host...
• Tophat errors with alignment summary and insertions data
  Hello, I have encountered a problem after using Tophat. I started off with fasta file of my geno...
• Running Cufflinks On Bacterial Rnaseq Data
  I am attempting to run Cufflinks on Galaxy main to analyze my E. coli RNAseq data. I have mapped...
• Create and extract consensus sequence after initial genome mapping using a custom genome
  I have aligned fastq sequences (from an insect vector) to a small bacterial genome of 1.2 mb (as...
• Hitsat2: Spliced alignment options
  Hi, I am trying to analyze RNAseq data with HISAT2. I would like to include spliced alignment. I...
• How do I get +/- strand orientation info from my RNAseq run?
  I made a RNAseq library using a stranded-RNAseq-library prep kit. The kit only amplifies the tran...
• Low alignment for paired end reads using HISAT2
  Hello, I am new to processing and analysis of RNAseq data. I have recently completed a paired-en...
• Reference genome for RNA STAR
  Hi, I am trying to use STAR for aligning RNASeq data but it doesn't have any reference genome. I...
• Why isn't HTseq on usegalaxy.org?
  Hello, I'm new to the public usegalaxy.org site. I was previously using a galaxy instance hosted...
• RNAseq data mapping to reference genome
  Hello, I have some RNAseq Illumina fastq data. I would like to align it to the referece genome o...
• what is thye meaning of too low aQual in Htseq
  I am doing the bacterial NGS data analysis and i ran the Htseq after Bowtie on my data. Can some ...
• Tophat Settings
  In the new version of tophat they allow for over 3 mismatches in the initial alignment, however y...
• No reference transcriptome
  I wish to perform RNAseq analysis and some of the alignment algoritms (kallisto, stringtie etc.) ...
• htseq-count returning only 0
  I'm trying to run htseq-count with Bowtie alignments to a bacterial genome. Even though almost 10...
• Joining Two Fastq Files With Overlap Reads
  I have a data generated from Miseq 2X250 bp these reads are overlap, before aligning to a my cust...
• Could you add reference genomes into the database?
  I got bacterial whole genome sequencing data from illumina and want to align them with reference ...
• Metatranscriptomic reads alignment and assembly
  Hello. I have a set of metatranscriptomic Illumina paired-end reads. I need to align them agains...
• Trouble With Rnaseq Analysis
  Hi everybody, I am trying to analyze the differential expression between two RNAseq samples. But ...