Similar posts • Search »

• Galaxy - Table Browser Fasta And Bed Format
  Hello, I got an unexpected scientific result from a simple "get data" from UCSC table browser wi...
• Sliding Window To Get Average Of A Seq Reads
  I have a bacterial genome which I divided into bins of 5 bp and counted reads in each bin. Now I ...
• Galaxy - Table Browser Fasta And Bef Format
  Hello, I got an unexpected scientific result from a simple "get data" from UCSC table browser wi...
• pileup --position in galaxy
  How do I get samtools pileup to work only on a certain set of positions (say a BED file)?
• Galaxy: Genomic Intervals to strict BED Conversion
  Hello: I'm new to the forum and Galaxy/bioinformatics. In the last two months I've been followi...
• Conversion GFF(3) to BED
  I am uploading a gff file for Toxoplasma Tgondii (GT1) organism on galaxy and try to convert this...
• mRNA expression Count
  Hi, I want to get mRNA expression count from RNA-Seq data. I am able to get gene expression coun...
• Bed To Wiggle?
  Is there an option to convert Bed file to wiggle file in Galaxy? Thanks
• Need help with "Count intervals in one file overlapping intervals in another file" tool
  Hi, I'm using Galaxy public on a windows computer. The 'Count intervals in one file overlapping ...
• Intersect output file
  Hi, When running 'intersect' to compare the ChIP seq data of 2 bed files to find overlapping si...
• What to do with Cuffquant .cxb files
  I would like to get a raw RNA-Seq counts matrix from the results of the Tophat alignment to a ref...
• Hg19 BED for CDS
  Hi I need to extract CDS from HG19 as BED and + strand or - strand /. can some one help - get da...
• How do I get ribosomal RNA counts from featureCounts of my bam files?
  Hi, I used HISAT2 to align more RNAseq fastq files and then featureCounts to count my features. ...
• Wig File Conversion
  I am a PSU student at the College of Medicine. I have minimal bioinformatics and computer progra...
• HiSAT2 alignment to GRCm38? in Galaxy -- where to find mm10 reference annotation
  I am doing an RNA-seq experiment and I ran HiSAT2 with the mm10 reference genome. Then in order t...
• voom normalized count data matrix (Differential count 0.3.0)
  Hi, I have used voom from the "Differential count" package and it worked smoothly. I would like t...
• Galaxy HTSeq tool give zero counts
  Hi, I tried galaxy HTseq tool on BAM file generated by HISAT2 to generated counts. I provided GT...
• No Mm5 Sequence Data In Galaxy 2.2
  when i try to download sequences for mm5 (uploaded bed file) i get an error: 4: Extract genomic ...
• Table With Gene Count Reads
  Hi, I was wondering if there is any tool on Galaxy were I can obtain a table with how many rea...
• Using Gatk Depthofcoverage With All Exon Enriched Data
  Hi, I have NGS results of DNA enriched for exons with an AllExon kit (Agilent). I have a bed fil...
• DEXseq count reads tool obtaining only zero counts for all exons
  I'd like to run DEXseq on my RNA-seq dataset to identify any potential differences in exon inclus...
• Peak Calling on BED files
  This is somewhat of a naive question. I've been using MACS2 on galaxy to call peaks on my ChIP-s...