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• How to visualize Bam Files normalize
  I have my DamID data (corrected by GATC fragments). I have two bams for Dam alone protein (the co...
• Obtaining a BED file for a NON-CODING chromosome locus
  I am new to Galaxy and do not know how to obtain a BED file for a NON-CODING chromosome locus (pr...
• Regarding reads extract from bam file
  Hello, Can anyone tell me that how can i get information of aligned reads using reads name from ...
• To determine frequency of crispr cas induced indels in bam files
  I have used CRISPR/Cas molecules to target a specific gene. I want to quantify the frequency of i...
• count and compare microRNA expression value in RNA-Seq data on Galaxy
  Hello, I have a question, I want to count and compare specific microRNA expression value in BAM ...
• SAM-to-BAM (NGS: SAMtools)
  I am trying to convert my SAM file to BAM file and I want to use the built in genome, but there i...
• Commandline SAMtools/BEDtools help!
  Hi all!  I'm trying to teach myself SAMtools/bedtools commands (on UNIX running on a VM). For pr...
• Dataset format conversion from fastq to bam and vcf
  Hello, I am a begginer in the galaxy and I want to ask you how can I convert fastq files to bam ...
• merging BAM files from within a list of datasets
  I uploaded three pairs of pairwise FASTQ files and combined them into a paired dataset list. Then...
• studying a locus for different variants of an expressed lnc-RNA
  I have done FASTQ groomer, Tophat and cufflinks on FASTQ data. Now, I want to study a pre-defined...
• conversion to Bedgraph files
  Hi, I have BAM files from Bowtie2. I want to use MACS2 bdgdiff in galaxy to identify differntial...
• featureCounts gives extreme low counts on highly expressed genes
  I mapped paired-end sequencing with RNA-STAR and got the BAM file. I then use featureCounts to co...
• Computing coverage from BAM file?
  Hi every one! I want to compute depth of specific regions from BAM file.I found two solutions li...
• Is it possible to have a tabular reference file for tools?
  I have a local tabular file that I want to use as a reference for a specific tool. Is this poss...
• Mapping quality plot of BAM file
  I'm interested in a specific genome region, is there a way/tool to make trackster track/plot/hist...
• How to pass the genome name or dbkey to a tool
  I'd like to pass the name or dbkey of a reference genome (e.g. hg19) to a tool . How can I set u...
• RNA-seq analysis in Galaxy
  I am doing RNA-seq analysis for several mouse samples and I encounter problems during differentia...
• How to create GFF file for HT seq
  Hello there, I am dealing with some RNA seq data and was trying to run the raw data in bam file f...
• Unable To Find The File
  Respected Sir / Ma'am, 'x' tool having 3 commands, 1) command takes files from path. ex perl x.p...
• chimeric transcripts detection tool
  Hi, How many tools can one find in the galaxy local too shed for detection of chimeric/fusion tr...
• Help with interpreting RNA-seq output
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• Galaxy Join of two large datasets makes duplicate rows, but same rows not duplicated when smaller file subsets are joined
  I'm using Galaxy, the Join tool. I've got two files, one a Locus ID and some data (file 1, ~220,0...
• Naming output file according to input file
  Hello, I currently develop a galaxy tool and I want to remove the extension from my input file. ...