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• 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...
• htseq-count crashed again and again
  htseq-count crashed again and again (Usegalaxy.org) Running output file from HiSat2, Runs fo...
• Error with htseq-count
  When I run htseq-count in galaxy I keep getting errors. The line in the history will look as foll...
• Reference Annotation Sources for RNA-seq tools
  When running htseq count, I got this error message: Fatal error: Unknown error occured [bam_...
• Duplicate row names error with EdgeR on FeatureCounts files
  Hi all, I created tabular count files using FeatureCounts with a GTF file (iGenomes, UCSC hg38) ...
• 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 processing GFF file
  Hi! I am running htseq-count for a RNA-seq and I got this error: Fatal error: Unknown error occ...
• 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...
• htseq-count unknown error
  I am trying to use htseq-count tool for gene quantification, but I have this error: **"Fatal err...
• 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...
• Reference annotation GFT GFF3 problem with tool HISAT
  I got the following error while running htseq count: I think it is my gtf file problem. How to fi...
• HTSeq-Count Error on Cloudman
  Hi I'm working on Cloudman doing RNASeq transcriptome analysis. I've made BAM file using TopHat2...
• 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...
• 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...
• Modifying GFF files
  Hi: I am working with a GFF file, which is missing 5' UTR annotations. I thought I might be able...
• 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: How to add id attribute and additional attributes in Galaxy (RNA-seq)
  Hello, I am working with a bacterial genome. I'm using DESeq2 for differential gene expression an...
• 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...
• Fatal Errors occurring with htseq analysis
  Hi, I am in the process of analyzing some RNAseq data. I uploaded the data and successfully mapp...
• Converting Ensembl GRCm38 gff to make it into UCSC format
  I am using STAR to align my RNAseq reads to UCSC mm10 mouse genome on Galaxy. Galaxy has UCSC mm1...
• htseq-count issues with Deseq2
  This is the first time im trying this but I keep running into issues. I'm running the htseq-count...
• Why does my GFF3 file not have any exons in the annotation lines read by HTseq-count
  When I ran htseq-count with my data. I am getting the error: Warning: No features of type 'e...
• 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...