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• SAMtools Merge BAM files hangs
  Hi all, I am using TopHat to map RNA-seq reads. My study species is a non-model organism, so I c...
• Mapping using multiple reference sequences
  Hi I am using BWA to map my FASTQ files against two different reference sequences (V3-1 and V3-2...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• Using different reference genome yields different results in RNA-seq data analysis
  Hello, I've got some questions with my RNA-seq results generated by galaxy.  For the experiment,...
• SnpEff supports only genomes of two species?
  Under usegalaxy, I was trying to use SnpEff to annotate my VCF, but the genome dropdown list show...
• Any computation limit? Bowtie2 job has been waiting for hours
  Hello. I submitted a job on Galaxy using Bowtie2 to map DNAseq reads onto sacCer3 reference genom...
• Convert genome coordinates between assemblies and genomes (Galaxy Version 1.0.5) aka LiftOver
  I have two related bacterial genomes of same species - different subspecies. I want to map the co...
• merging two unrelated reference genomes and annotation files
  Hi, I work with an intracellular pathogen. I would like to run an RNA-Seq analysis in galaxy usin...
• 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 ...
• Get multimapped reads from STAR in Galaxy.
  Hi, Using RNA STAR in Galaxy to map my yeast read back to the genome: (single end reads), I'm g...
• An error occurred setting the metadata for this dataset
  Hi Galaxy Team, I've been using TopHat to map my reads and I've received the same error message ...
• Low mapping of paired-end reads with tophat2
  Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage...
• Bowtie mapping result
  Hello, I used "Map with Bowtie for Illumina" tool to map the sequences reads to the reference ge...
• Bfast For Solid Paired End Reads
  I am new to RNA-Seq and trying to map ABI SOLID paired-end reads. I've read that BFAST + BWA is ...
• Preprocessing Gdna Illumina Paired End Data For Mapping/Snp Calling
  This question is w/ regards to pre-processing whole genome resequencing data for mapping data to ...
• bam to fasta
  Hello, I am very new to dealing with NGS data.  Have followed the instructions on how to get pai...
• How to get only paired end or single end uniquely mapped reads with Bowtie2?
  Hello, I am using bowtie2 on galaxy to map ChIP-seq single end and paired end libraries to a ref...
• using mPileup to examine allelic imbalance in hybrids
  Hi, I have some RNA-seq data for two different species and their hybrids. I want to look at the ...
• Bwa Failing To Index?
  I just installed a new instance of Galaxy and bwa_wrappers from the main toolshed. I then upload...
• Join On Genomic Interval
  Hello, I am hoping for some clarification on how Join on Genomic Intervals functions. I have two ...
• Can Galaxy Help With Comparative Genomics?
  The lab I work with would like to compare a few populations' genomes of a species with an unpubli...
• HISAT seems to assign wrong XS tag value to some reads of stranded RNAseq data
  Hi All, I have some paired end stranded RNAseq data prepared using an Illumina TruSeq Stranded m...