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• Need to GFF file for RNA-seq analysis
  Hello, I am doing RNA-seq analysis using use galaxy.org, I want to run htseq but I do not know...
• htseq-count unknown error
  I am trying to use htseq-count tool for gene quantification, but I have this error: **"Fatal err...
• Modifying GFF files
  Hi: I am working with a GFF file, which is missing 5' UTR annotations. I thought I might be able...
• Error with htseq-count
  When I run htseq-count in galaxy I keep getting errors. The line in the history will look as foll...
• Fatal Errors occurring with htseq analysis
  Hi, I am in the process of analyzing some RNAseq data. I uploaded the data and successfully mapp...
• Inputs not recognized by tool
  I have uploaded two bam files to Galaxy to generate HTSeq counts. However, both my bam file and g...
• HTSeq-Count: Maximum alignment buffer size exceeded while pairing SAM alignments
  Hi I'm working on Cloudman doing RNASeq analysis. I am trying to use htseq-count tool for gene q...
• Error: htseq-count exceeds memory buffer, Solution: Set sort option on tool form to Yes
  Hello, I am dealing with RNA-seq data and I was successfully able to align my raw FASTQ data to t...
• 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...
• Error in Galaxy - ''Fatal error: The HTSeq python package is not properly installed, contact Galaxy administrators''
  Hi I'm trying to run HT_seq Count with some BAM files and a GFF file but keep getting this error...
• htseq-count error with strand data
  Hi! I am running htseq-count for a RNA-seq and I got this error: Fatal error: Unknown error occ...
• Htseq-count input data
  Dear colleagues, I am a new Galaxy user motivated to exploit its tools to compare two sets of the...
• htseq-count failed with error no exon found
  I am having trouble with htseq-count. My gff file i.e. [brassica juncea .gff file][1] does not co...
• htseq-count with gff error
  Dear all. Please take a look at my errors: http://goo.gl/Oa2IxR In the link, you will see 2 ima...
• Htseq-count error: [Errno 2] No such file or directory: 'name_sorted_alignment.bam'
  Dear all, I am facing this error while running HTseq-count on a BAM file obtained with Tophat: F...
• What does this HTseq-count error mean?
  I am running HTseq-count on galaxy cloud on some BAM files generated from galaxy Tophat. But I go...
• DESeq2 ascii codec can't encode character
  Hello everyone, I have this error when I try to use DESeq2 1.8.2 from iuc team : https://gist.g...
• Wig File Conversion
  I am a PSU student at the College of Medicine. I have minimal bioinformatics and computer progra...
• Reference Annotation Sources for RNA-seq tools
  When running htseq count, I got this error message: Fatal error: Unknown error occured [bam_...
• htseq-count no read align
  Hi I am trying to get raw count of mapped read, so I am running htseq-count on tophat accepted h...
• Impossible to use Htseq-count on BAM files from Tophat2
  Hello, I'm currently facing troubles using galaxy. I want to compare differentially expressed ...
• 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...
• Conversion GFF(3) to BED
  I am uploading a gff file for Toxoplasma Tgondii (GT1) organism on galaxy and try to convert this...
• Expected Transcriptome Blast
  Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcri...