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• Mapping paired reads to reference genome, variant calling
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• FASTQ Joiner or Interlacer problem
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  I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joine...
• Multi Fastq joining
  Hi All, how to join multi FASTQ left-hand reads or right-hand reads together? I need map sequence...
• fastq joiner and tophat
  Hi,   I have paired end reads of two samples and i used FASTQ joiner to join them, now i want t...
• 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...
• 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...
• 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...
• Fastq Joiner Problem
  Hi, I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq j...
• Count intervals of non-uniquely mapped reads overlapping the genome
  Hello everyone, I have some SAM/BAM files containing the alignments of small RNA-seq reads to mm...
• Need help with "FASTQ joiner" tool
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• Pre-Processing Of Illumina Rna-Seq Paired End Data
  Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically ...
• Converting pair-end dataset to fastq
  I'm new to galaxy and am trying to use the cloudmap workflow to conduct "Hawaiian variant mapping...
• Illumina HiSeq reads and Fastq joiner
   Hello, I have paired-end reads (Illumina HiSeq) from a metagenome in two Fastq files. These non...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• Barcode Splitter On Paired End Reads
  Dear Galaxy team,   I am sorry for repeatedly asking this question but I would like some feed bac...
• Fastq Joiner Fails To Join Pe Data.
  Hi, I have HiSeq2000 paired end sequence data in two separate FASTQ files. I need to filter t...
• Filtering BAM files from HISAT2
  Hi. I am new to rna-seq and I have a couple of quick questions. My input was paired-end non-stran...
• Error using stringtie - AttributeError: 'NoneType' object has no attribute"
  Hi, I have **RNA-seq data** and I am interested in whole gene expression results but also transcr...
• Trouble with FASTQ joiner
  Hi Biostars community, I attempting to run some initial QC and manipulation tools on some rnaseq ...