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• Need help with "MACS" tool--program setting
  Hi, I have a question about running MACS tool for my chip-seq data to call the peaks for the tra...
• trimgalore on interleaved paired-end fastq files
  Hi, I'm analyzing interleaved paired-end fastq files downloaded via fastq-dump. I am trying to r...
• Splitting Biased Paired End FASTQ data
  The FASTQ splitter in Galaxy warns that the tool only works if Paired-end data has equal length r...
• MACS and BDGdiff
  Hi, I run MACS2 with broad and paired-end settings, but it did not produced any lambda files whi...
• 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 ...
• 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?"...
• Aligning more than 2 sequences
  I have a pair-end data fast1.fq and fast2.fq in (fastq format). Now, I need to align the pair-end...
• Merging Of Illumina Paired End Files
  I have 3 illumina paired end reads of exome capture of the sample. I want to assemble these reads...
• How to split a merge piared data using ncbi SRA tools?
  can I split a merged paired end extract reads into two separate data (acc. to their ends) using n...
• Initial Qc And Grooming For Illumina Hiseq2000 Paired End Rnaseq Data
  I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files f...
• Question About Using Bowtie
  I am trying to use bowtie to assign reads to the s. Cerevisiae genome. I have data from paired en...
• 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...
• Data collection and Tophat2
  Hi, I am trying to play with data collection (developped by John Chilton) and I am confused on h...
• Can we map fastq files with paired ends using bwa mem on galaxy?
  I have a collection of timmed fastq files from WES, each contain paired ends. Is it possible to m...
• Paired End FASTQ files
  Hi all, I have a question regarding paired end FASTQ files for chip-seq analysis. Which followi...
• MACS gives the same output using different inputs and with no input
  Hi, we use MACS to call peaks for all of our ChIP-seq data and it has never given us any problems...
• History not found when logged in
  I am using galaxy to analyze ChIP-seq. I created log in account. I could see Bam and Bigwig file ...
• Fastq Quality Trimmer For Pe Illumina?
  Hello, I was wondering, can Galaxy's FASTQ Quality Trimmer tool be used on Illumina paired-end d...
• Genome Assembly With Velvet in Galaxy
  I have found data for E.coli sequencing reads. Following are paired end reads of E.coli ftp://f...
• Converting pair-end dataset to fastq
  I'm new to galaxy and am trying to use the cloudmap workflow to conduct "Hawaiian variant mapping...