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• Problem With Depth Of Coverage On Bam Files (Gatk Tools)
  Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The interva...
• BAM files fail to be recognized
  I generated BAM files on galaxy using BWA-MEM. I am trying to run BAMtools, Picard, etc on them. ...
• Problem With Gatk Tools Not Accepting Bam File As Input
  I am using GATK tools on the useGalaxy main server to detect variants in a mutant C. elegans whol...
• Analysis 454 Quality Data
  Hi, I am starting off with 454 read data in an sff file. I would like to get quality statistics ...
• Need help with "Create a BedGraph of genome coverage" tool
  Hi there I am trying to calculate the coverage of my alignment based on the BAM file using "Crea...
• Bam to BigWig conversion fail
  I tried converting my sorted bam files to bigwig (my build is mm10) and got this error: 1 is ...
• Error: Unable to access jarfile /please/GenomeAnalysisTK.jar
  Hello, I tried to use Depth of Coverage (version 2.8.0), but I got the following error: Error: ...
• Depth of coverage in one nucleotide
  hi I want to find depth of coverage in one position, for that I used GATK tools, but I give one e...
• multi bam summary
  Hello, I was trying to use mutibamsummary tool to generate the read coverage for 8 filtered Bam ...
• HELP!! BAM file shows one line analysis with zero values when "bam coverage" is run
  Hi I have uploaded four BAM files to the galaxy. I ran BAM coverage on them with 100 bin. One fi...
• Problems Adding A Custom Build
  Hi, I am having problems that I think are related: *1. * I have not been able to visualize (in ...
• Bedtools coverage not accepting file b
  Bedtools coverage does not accept the -b files. Compute both the depth and breadth of coverage o...
• Extract depth coverage of a particular region from BAM file
  Hi, If any kind soul could help, I loaded BAM files in IGV and i notice some interesting splicin...
• .Bam File Upload And Use Problem
  Recently I was trying to use Galaxy for my data analysis but ran into problems..... Condition: I...
• Sam To Bam Conversion Problem
  Hello Galaxy Support, I generated an alignment with a "fastq groomed" illumina dataset using the...
• sam to fastq
  Hi I have mapped PE reads to a custom build genome using bwa and converted the sam output to bam...
• Error On Custom Builds On Public Galaxy Server
  I am having a problem with the public galaxy server. When I try to go the User->Custom Builds...
• Computing coverage from BAM file?
  Hi every one! I want to compute depth of specific regions from BAM file.I found two solutions li...
• MACS2 run error
  Hello to anyone willing to help, I tried running Bowtie2 bam files on MACS2 to get peaks, howeve...
• SAM-to-BAM 'Failed runtime validation of Using reference genome' Error - Local Galaxy instance
  Hi, I'm trying to run a workflow on a local Galaxy instance that has these steps in the beginnin...
• Cuffdiff Error after cuffmerge or cuffcompare
  Hi everyone, I'm doing a transcriptome of zebrafish, 2 replicates for each condition of 3 conditi...
• Multiple input for samtools mpileup (-b option) for GBS pipeline
  Hello, I'm working on an GBS analysis workflow which was previously designed for command line usa...
• Input For Gatk Depthofcoverage
  Hi Galaxy Team, I'm trying to use GATK DepthOfCoverage, and to give a BAM file of alined results ...
• what features are counted by 'compute both depth and breadth'?
  I used the bed tool Compute both depth and breadth of coverage', but it is not clear to me whethe...
• Mm7 Chromosome Name
  Hello, I have a set of coordinates for mm7 that I have been using try to extract the genomic seq...