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• Bam to BigWig conversion fail
  I tried converting my sorted bam files to bigwig (my build is mm10) and got this error: 1 is ...
• Displaying bam or bigwig files in UCSD genome browser
  Hello, I am attempting to view my RNAseq mapping file output (SAM) on the UCSC genome browser. T...
• Bam file can not convert into bigwig
  Hello, I got a bam file and upload to the Galaxy.  When I convert it into bigwig, it gives me th...
• Convert BAM into bigwig for chicken
  Hi, I used functions of “Create a BedGraph of genome coverage” and “Wig/BedGraph-to-bigWig” in G...
• Need help with RNA-seq quantification
  Hi Galaxy Support,   I want to use cufflinks to quantify my own  bam file, which is not from ga...
• Put header to bigwig file
  Hello, I am working with ChIPseq with Histone marks on chicken (Gal/Gal4). I generated a bigwig ...
• Recent problems writing Bigwig from Bam files
  I am having problems writing BigWigs using the convert command from an uploaded STAR Bam file. A ...
• bam to stranded bigwig?
  Hi, I have a bam file generated from stranded RNA-seq data - is it possible to use galaxy to spli...
• File Uploads
  I am trying to upload .bam and .bigwig datasets, from geo, into galaxy. Galaxy will not recognize...
• Bam to Bedgraph error
  Hello, I am trying to convert bam files to bedgraph files and eventually to bigwig to visualise ...
• Normalization when convert bam to wig
  Hello, I am new to the bioinformatics analysis, I want to display bam coverage in IGV to show the...
• Bam To Bigwig
  Hello, I am trying to convert a BAM file to Bigwig using the Convert Format option under Attribu...
• Viewing BIGWIG files in UCSC
  Hello, Previously I have been able to view BigWig files by clicking on the job, and selecting Di...
• 'Sampling' Bam or BigWig files?
  I am involved in an RNAseq project in which mutliple tissues of an organism are being analysed. N...
• Chrom len file bedgraph to bigwig
  What is the best tool to use or where can .len files be found for the bedgraph to bigwig tool. I ...
• wig to bigwig
  Hi Galaxy, I am trying to convert 12 Wig files to bigWigs since 7PM on Saturday. Conversion work...
• Error of wig/BedGraph-to-bigWig converter
  Hi, I have a ChIP-Seq BAM file aligned on the chicken galGal3 reference genome using Bowtie2. I ...
• Convert Sam To Bigwig
  Hi, What is the 'official' method of converting a BAM file to a bigwig on the public server? I ...
• Cufflinks Help
  Hi All, I am trying to analyse some human RNA-seq dataset which is in BAM format to generate FPK...
• Wig/BedGraph-to-bigWig fails with "hashMustFindVal: '1' not found Error running wigToBigWig."
  Hi, I have a very large, merged BAM file which I successfully converted to a bedgraph using the ...
• How to use data from Roadmap epigenomics project to run ChromHMM
  I am new to this area. I am now trying to utilize the data from Roadmap epigenomics project (link...
• Galaxy update errors
  I have recently updated Galaxy to the latest release and I am having a couple of issues. 1. When...
• DiffBind differential binding analysis of ChIP-Seq peak data
  Hi, I am analysing ChIPseq data on Galaxy beginning with raw fastq files (fastqc, trimmer by col...
• Comparing FPKM Values Between 2 Cufflinks Outputs
  Hello, apologies if this is a dumb question, I am relatively new to RNAseq. I have processed 9 sa...