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• Running Trimmomatic on loop for Paired End
  I'm need to do trimming for Paired End. Is there any way around where I can run the trimmomatic ...
• Help! I'm using trimmomatic in Galaxy, but it doesn't recognize a part of input dataset.
  I'm using Trimmomatic to trimming paired end reads. When I set "Single-end or paired-end reads?"...
• Mapped paired-end reads with Bowtie2
  Hi Biostar community, I have paired-end reads for MeDIP-seq. I'm able to mapped read1 and read2 ...
• Paired End FASTQ files
  Hi all, I have a question regarding paired end FASTQ files for chip-seq analysis. Which followi...
• cuffmerge for single end and paired end
  is it correct to merge the single end and paired end data together in cuffmerge? if yes then why ...
• trimmomatic with paired-end
  Dear Biostar, I have paired-end sequencing data I would like to trim using trimmomatic. I have r...
• Use paired collection on wrapper
  Hi, I'm try to write a wrapper for a tool that performed subsampling of fastq file. The script i...
• Structurefold Iterative Mapping Input Fastq
  Regarding the tool structurefold, iterative mapping on Galaxy accepts one fastq at a time as inpu...
• RNA STAR job error
  Hello, I am trying to RNA STAR aligner on pair end reads with inbuilt index but I am getting err...
• Trouble loading fastq data
  Hi, I have difficulty uploading one of my input file for a pair-end (two separate input files)....
• Paired-end dataset collection with Bowtie2
  Hi, I made a paired-end fastqsanger dataset collection and tried to run it with Bowtie2, but it ...
• 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...
• MACS shows error for MEDIP Seq Data
  Dear sir, I tried to do peak calling for Medipseq Data using MACS. i have done mapping using Bo...
• ChIP-seq paired-end analysis
  Could you help me to understand how to analyze the data CHIP- seq paired-end on galaxy ? Thank y...
• Data collection and Tophat2
  Hi, I am trying to play with data collection (developped by John Chilton) and I am confused on h...