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• Can I Convert Paired-End Datasets Into Single End Ones?
  Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inn...
• 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 ...
• 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...
• Paired End FASTQ files
  Hi all, I have a question regarding paired end FASTQ files for chip-seq analysis. Which followi...
• Cufflinks Fpkm
  Hi, I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the e...
• combining indexed paired reads from two lanes of a Hiseq rapidrun
  Hi I am doing paired end RNAseq, I have a single multiplexed pool that was run over both lanes o...
• Pair end alignment using HISAT2
  Hi, I have a FASTQ file that is a paired library. I want to align this FASTq file to Hg19 genome...
• Normalization on Single End and Paired End reads
  Hi there. I want to assemble a transcriptome with Trinity using reads that are both paired- and ...
• 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...
• Markduplicate single end reads miRNA seq data
  I am trying to analyze a RNA seq, single end SRA dataset. For this do i have to perform Markdupli...
• mm10 built-in reference genome unavailable
  Hi, I'm trying to run cuffdiff with bias correction: perform bias correction 'yes' -> Refer...
• 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...
• Issues On Rnaseq Since The Changeover
  My histories seem to be stopping their processing around the Tophat-cuffmerge steps since the cha...