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• Can contamination cause alignment errors and how can I trim contaminants away?
  Hello Galaxy Team, Sorry if this question is all over the place. I have been trying to align ...
• Counting Rna-Seq Reads Per Class.
  Hi All, I have been trying to count the number of RNA-seq reads that fall into the various Cuffli...
• Counts per million to differential expression
  Hi All, Strange question so a bit of background: I have used a targeted RNAseq panel so it is e...
• Need help with 'barcode splitter'
  I have a Fastq dataset obtained from Miseq with 24 million reads. When I use the barcode splitter...
• comparisson of RNA-seq FPKMs across samples
  Dear BioStars community, I am trying to "recycle" some RNA-seq data published as supplementary m...
• Can Galaxy Help With Comparative Genomics?
  The lab I work with would like to compare a few populations' genomes of a species with an unpubli...
• Re: Pilup File And Counting Reads In 200Bp Windows
  Hello Di, Once the data is in pile-up format, the read identifier is lost, so summarizing per-re...
• Why gene counts from RNA STAR don't match total uniquely mapped counts
  Hi, I used RNA STAR to map my reads for a stranded-RNAseq library. Within RNA STAR, i turned on...
• Compute tool - invalid lines?
  I'm working with two files that contain nucleotide count data from the 'variant annotator' tool. ...
• About rarefaction curve : FROGS pipeline
  Hello everyone, I am doing a metagenomic analysis on Galaxy with the pipeline FROGS. Everything ...
• SICER Failed to
  I have been trying to run SICER on my ChIP-seq data set. Seequnces were aligned with bowtie2, seq...
• Mapping Unmapped Sequences To Other Guessed Contaminants
  Hi, I am a relatively new user to Galaxy. Of the 21 million mappable illumina reads, 17 million ...
• Less reads when uploading to galaxy
  Hello, I am trying to upload files which contains, each, about 40 millions of reads (~2GB each, ...
• I am slightly confused about the input requirements for the differential expression tool - last step of Trinity
  Hello all, I have a pressing question... To start with, I have read the Trinity methods paper ...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• (No Subject)
  Hi Dear Is there anybody whom I can share my data with? I have an important question that I trie...
• Tool barcode splitter not recognizing inputs (PEAR-assembled reads)
  I ran an Illumina 2 x 250 PER on PCR amplicons and received the data demultiplexed by the Index o...
• Total genomic DNA Concentration for cows (healthy and infected) milk microbiome study
  I have extracted DNA from cows milk using Promega FFS Nucleic Acid extraction kits and Promega bl...
• mapping RNA-seq reads with "N" in the middle of each read
  Hi all, I am performing differential gene expression analysis using the Tophat-Cuffdiff protocol...