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• Featurecounts for paired end RNA-seq reads not generating counts
  Hi I have paired end RNA-Seq reads that I aligned to my reference genome using HISAT2 (alignment...
• Error occuring in CleanSam after alignment with Bowtie2
  Hi, I am just starting to get familiar with Galaxy and bumped into a problem of which I don’t kn...
• FASTQC issue getting error in web page
  Thank you for that. I did finally upload my sequence using the file zilla. First I changed my .gz...
• Trinity results mismatch during alignment
  Hello Jen I thank you for your help. I think I have understood why there is a mismatch. I run de...
• X. laevis v9 genome alignment on galaxy
  HI, Could you upload the x. laevis v9 genome available at Xenbase (ftp://ftp.xenbase.org/pub/Geno...
• Trimmomatic output results in extremely low alignment using bowtie2
  Hello, I have trimmed by paired end data RNA seq (Illumina Miseq) data using trimmomatic. Howeve...
• error using HTseq-count for conversion of .bam to raw counts
  Hello, I am trying to convert the .bam files I got as output from tophat alignment into raw coun...
• Aligning more than 2 sequences
  I have a pair-end data fast1.fq and fast2.fq in (fastq format). Now, I need to align the pair-end...
• Built-in indexes not working in Local Galaxy Instance
  Hi, I've just finished setting up a local Galaxy instance and everything works fine except for b...
• RNA STAR job error
  Hello, I am trying to RNA STAR aligner on pair end reads with inbuilt index but I am getting err...
• Missing fields in Picard 'Collect Alignment Summary Metrics' tool(s)?
  HI      When I run the Picard  'Collect Alignment Summary Metrics'  on usegalaxy.org on either...
• Maq Output
  Does anyone know if Maq can produce alignment data in SAM format? Currently we can only generate ...
• Is the RNA STAR aligned file already been sorted?
  Also, I see unknown contigs that are not present in my chosen reference hg38 gtf file (Gencode.v2...
• Expected Transcriptome Blast
  Hey, Jack Colicchio here, a PhD. student at KU. I am about to get an illumina Next gen transcri...
• Waiting to run for 6 days
  I submitted 6 fastq files to be aligned using Tophat 6 days ago. 5 were aligned within 24 hours. ...
• Saccharomyces cerevisiae reference genome for TopHat,Bowtie
  Hi, I am new to Galaxy, and for my first project I wish to analyze some sequences we recently ob...
• ANNOVAR annotate cuts short the VCF file ?
  I uploaded a standard VCF that contains 57651 lines (or 57471 lines variant data) and ran it with...