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• RefSeq Annotation using SnpEff
  Hello, I am working with human whole genome sequence. I have called variant using samtools and I...
• Need help with "ANNOVAR Annotate VCF" tool
  Hi there, When I open Annovar annotate VCF tool on Galaxy I cannot visualize any option for the ...
• Gene name annotation
  Hi, I've done cufflink-> cuff merge-> cuffdiff finally, I used reference annotation huma...
• VCF gene name sorting
  Hello, I have a vcf file and need to tie it to the gene name. I did this with the vcf annotate t...
• ANNOVAR galaxy returning an empty file
  I am working through a project that requires me to Identify genes with polymorphic sites using AN...
• snpEff gene names
  Hello! I am new to snpEff. I built my database for my sample using gff3 files created from PROKK...
• Gene annotation for cuffdiff/cufflink
  I was wondering how to get gene "name" annotated to the cuffdiff. I used mm10 as the template, an...
• How can I annotate a vcf file created with Freebayes with rs#
  Hi All, I have a vcf file created in freebayes (v.0.0.2), and I would like to annotate the file...
• How to convert gencode ID into ENSEMBL ID
  Hi, I have gene Id derived from gencode and I am trying to convert into gene names, but i think I...
• How Insert Gene Ids?
  Hi, I have used the RNAseq tools to calculate the FPKMs values, now I would like to know how I c...
• Annotation file formats .gff3 to .gtf conversion
  Dear all, I used the Galaxy tool to convert the .gff3 annotation file to .gtf format. Going thro...
• Batch conversion of ID to gene symbol
  I'm an old school molecular biologist who studies gene expression but is quite new to bio-computi...
• gene names from ucsc id
  i have cufflink and cuffdiff output. i want gene names in ncbi ids and a tabulated format. i can ...
• gene names from a vcf annotate file
  hi i need an answer. i have a vcf file and i want to see gene names on each chromosomes in the v...
• Which tools can be used for gene annotation and for determining zygosity?
  I am unable to find VCFannotate tool in Galaxy and if I am using AnnovarAnnotate I am only gettin...
• convert annovar in excel to vcf for igv viewing
  Hello, In an excel file I have the chromosome, start and stop positions, reference allele (Ref),...
• how to get gene name in varinat anlysis results
  hellow sir/ madum i got vcf file ofter running freebayes ,i got position of the gene actully i ne...
• Need help with "ANNOVAR Annotate VCF" tool
  Hi!  I entered a vcf file into the annovar tool.  It looks like it ran and tells me then number o...
• htseq and cufflinks
  Hi, I have used HTSeq to count the no of mapped reads, the HTSeq gives me the ensemble ids but w...
• Cuffdiff output redundant genes
  Hello, I am using the Galaxy tool Cuffdiff to analyze the RNA-seq data. But for the output file "...
• Filtering A Vcf File
  I’m using a local instance of Galaxy. I’d like to filter a VCF file for SNPs that have passed fi...
• Tss List With Annotation For Hg19
  I want to extract TSS ids with correspodning location for Hg19. Once I extract such TSS coordina...
• DAVID missing from the Galaxy toolshed?
  Hi everyone, I have noticed that the DAVID wrapper is not available on the Tool Shed, despite th...
• Normalization An Dplotting Of Rpkm/Fpkm After Cufflink
  Hi,   I want to include the following discussion in my message regarding use Bam files of To...
• How to covnvert gene id to gene names
  Hi, I have been using Tophat, cufflink, cuffmerge and cuffdiff to analyse RNA seq data. I hav...