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• Re: Quality Based Trimming
  Thanks for your reply Daniel. That's right... I did not even think about using the boxplot tool t...
• Trimmomatic Operation Error
  Hi, I try to trim my sequence with trimmomatic. But I cannot understand why my options are not ta...
• Problem with FASTQ Quality trimmer by sliding window
  Hi, I´m using the FASTQ Quality trimmer by sliding window with a quality score of 25, and after r...
• How To Count Reads In 200Bp Windows And Save The Output Per Chromosome?
  Hi all, I recently have some Gro-seq data. What I want to do is this: 1. Workflow Counting how...
• Question Regarding: Fastq Quality Trimmer
  Hello, I am running Galaxy locally and it has been performing flawlessly! I wanted to get more...
• Comparing Data Sets With Different Coordinates
  Hello, May I use galaxy to do correlation analyses with two continuous quantitative data sets co...
• 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 ...
• Reads with failing Kmer enrichment in FastQC - priming bias?
  Hi there! I am performing a quality check in a transcriptomic dataset before attempting a de-nov...
• Help! Galaxy MACS Peak Calling-
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• 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...
• Depth Command In Sam Tools
  Dear all, I am a Phd student working on chicken genomics, with limited experience in the bio-inf...
• Operate On Genomic Intervals
  Hello, I have binned the mouse genome into fragments based on restriction enzyme cut site...
• SICER Failed to
  I have been trying to run SICER on my ChIP-seq data set. Seequnces were aligned with bowtie2, seq...
• How to calculate the Average Insert Size after mapping the reads to the reference genome using BWA
  Hi everyone, Having mapped the reads (paired-end) to a reference genome using BWA, I am trying t...
• How to calculate SNP density for sliding windows across a VCF file in galaxy?
  Hi  I am trying to think of a way of calculate the number of SNPs per 5kb sliding windows across...
• multibamsummary vs multibigwigsummary
  I am in the process of comparing the similarity between two ChIP-seq conditions. According to the...
• Regional Variation Make Windows Output
  i believe there is an issue with make windows tool: i am attempting to create sliding windows on...