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• Are reads number normalized on transcript length ?
  Hello, I used featurecounts to obtain reads number from a RNA-seq file (.bam). I would know if t...
• rmdup - remove PCR duplicates from ChIP-seq data
  I have aligned my chip-seq data with bow tie and wanted to remove PCR duplicates. I ran rmdup in ...
• 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 ...
• Trimming Illumina Reads From 3' Without Considering Quality Score
  Is it possible to trim certain number of bases from 3' end with taking into consideration quality...
• Chip-Seq Normalization To Total Number Of Reads
  Dear Galaxy, I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 datase...
• Extracting Number Of Reads From Bowtie Analysis
  Hello, I am new here! I am aligning Solexa files to genome using tool: NGS: Mapping: Map with Bo...
• 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...
• Extracting Reads Mapped From Bwa Mapping
  Hello, I recently figured out how to filter the output bwa SAM file for flag type in order to de...
• Trimmomatic Operation Error
  Hi, I try to trim my sequence with trimmomatic. But I cannot understand why my options are not ta...
• Number of sequence reads
  Is there a simple way to determine the number of sequence reads in a file uploaded on Galaxy and ...
• How can I see the amount of reads and aligned reads from Bowtie?
  Hi, I am trying to see the amount of reads produced by Bowtie and also the number of aligned re...
• Re: Output File For Bowtie Suppressed Reads (-M/--Max)
  Hi all, I'm running into a problem with the output from bowtie mapping for illumina reads. I'v...
• ERROR MESSAGE: Your input file has a malformed header: VCFv4.2 is not a supported version - Eval Variant Tool
  Hi, I am getting this error when running eval variant tool from GATK ver 2.8 in galaxy. ERROR...
• Bug For Mate Pairs Colorspace To Sequence Conversion
  Hi, I have a problem converting paired reads with paired end reads from ABi, in the color code t...
• Question
  Hi Is it possible to trim a variable number of a specific nucleotide from the 3' ends of fastq R...
• Counting Rna-Seq Reads Per Class.
  Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cuffli...
• Fastq Joiner
  I am trying to join two groomed fastq files from a paired-end Illumina read using the fastq joine...
• 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 ...