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• Fetch Alignments using Stitch Gene blocks, but '-' strand has been joined wrong
        As I use Fetch Alignments => Stitch Gene blocks extract genes from the maf file accordin...
• Cuffdiff Without Gene Annotation
  Hello guys, I went through the RNAseq workflow (I didn't do Cuffmerge) and from the Cuffdiff outp...
• Query Related To Lift Over
  Hi all,I have data with RGSC 3.4 build, along with the start and end coordinates of genes. I want...
• How to make negative values positive for t-test
  Hello everyone, I have an microarray data and I want to use volcanoplot (with t-test) in Matlab b...
• pileup --position in galaxy
  How do I get samtools pileup to work only on a certain set of positions (say a BED file)?
• Star-Fusion: A last-matching gene pairs file - in Galaxy you can create such files with the ncbi_blast_plus tool suite containing blastn: ....
  I am running Star-fusion on rat genome Position: A last-matching gene pairs file - in Galax...
• negative and positive fold change for a set of unigenes with similar gene ids in a single condition
  I am struck with a little thing. I have differential expression from RNA Seq data from two condit...
• 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...
• Chip-Seq And Gene Ontology With Galaxy-Ucsc
  Hi, I am currently doing some ChIP-Seq experiments, to analyze the data I get from the PeakFinde...
• 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...
• 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...
• Q About 'Compute' Tool
  Hi, Can 'if' statements by used in 'Text manipulation' > 'Compute'? The reason is that i hav...
• finding the number and positions of exons and introns
  hi I have a CDS sequence and I need to know about the number and positions of exons and introns C...
• How To Find The Alternatively Spliced Segment Of Genes In Cuffdiff Output
  Dear All, I have run programs from Tophat to Cuffdiff of Galaxy to look for the difference in al...
• How To Sort Mapped Data?
  Hi everyone, I am working on RNA-seq data. First, I mapped the reads to the reference transcri...
• rsID from list of chromosome and position
  Hi, I wonder could I create a list contain Chromosome number and a column for position (in build...
• How To Extract Geneid From Pileup File?
  Dear galaxy-users, I am working on a project to identify and genotype SNPs in targeted genes. ...
• Shifting two inputs
  I have two inputs and would like to change their positions (input #1 becomes input #2 and vicever...
• ChIP-seq workflow help
  Hello, I am a rookie of processing ChIP-seq data, I get a dataset which is about neuroblastoma. ...
• Extract Alignment For A Set Of Genes
  To Whom It May Concern, Sorry to bother you with what is likely a fairly simple problem, but I h...
• Extract Data And New Genes
  Hi Everyone, I am working with *Aedes aegypti * and I obtained around 500 million reads (HiSe...
• Fw: Chip-Seq And Gene Ontology With Galaxy-Ucsc
  I actually did an exercise that described how to get GO IDs and GO terms from UCSC Table Browser ...
• Remove sequences with duplicate chromosome start position
  I used GALAXY to extract the 1000 bp upstream of all UCSC genes (i.e. promoters). I sorted the da...