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• Fastq Quality Trimmer For Pe Illumina?
  Hello, I was wondering, can Galaxy's FASTQ Quality Trimmer tool be used on Illumina paired-end d...
• Considerations for trimming poor quality Illumina MiSeq paired end reads
  I have generated fastq files from Illumina MiSeq for bacterial genome sequencing. My reads are 2...
• Kraken (assign taxonomic label...)
  One Illumina file fastq.gz contain all info about paired-end reads. I used by usegalaxy interface...
• Can I Convert Paired-End Datasets Into Single End Ones?
  Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inn...
• Too few reads after VarScan on RNA-Seq data?
  Hi all, I have been trying to initiate a protocol to call SNPs in RNA-Seq data, but have had a f...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• Paired end illumina RNAseq reads - running trinity with paired trimmed files and adding unpaired as single read?
  We have paired end Illumina HiSeq 4000 reads that we are working to remove adaptors and trim base...
• Illumina HiSeq reads and Fastq joiner
   Hello, I have paired-end reads (Illumina HiSeq) from a metagenome in two Fastq files. These non...
• Need help with "Tophat for Illumina" tool
  Dear All, Hello amazing Galaxy team members  now i have 14 manipulated fastq files 7 forward an...
• Problem in cuffdiff
  Hi everyone...after doing cuffdiff when viewing the data in tabular format of gene differential e...
• Fastq Splitter Empty And Fastq Manipulator Doesn'T Work
  I am having the same issue as this user: http://user.list.galaxyproject.org/FASTQ-splitter-produ...
• Combining The Paired Reads From Illumina Run
  Hi, I have two fastq files with the forward(/1) and reverse(/2) paired reads. The reads are not ...
• Merging Fastq Files
  Hi I have received Illumina paired-end genome sequence data as a .tar file. When unpacked the dat...
• Convert multiple FASTQ files into one BAM file
  Hello guys! I recently started working with NGS analysis and I may have a stupid question to ask....
• Trimmomatic output after filtering paired end data - fastqsanger vs fastqsanger.gz
  After running Trimmomatic on a paired end PolyA RNA-seq dataset where both forward and reverse re...
• Realigner Target Creator will not run?
  I have been running the pipeline below to try and call SNPs from RNA-Seq data but have encountere...
• Initial Qc And Grooming For Illumina Hiseq2000 Paired End Rnaseq Data
  I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files f...
• HISAT seems to assign wrong XS tag value to some reads of stranded RNAseq data
  Hi All, I have some paired end stranded RNAseq data prepared using an Illumina TruSeq Stranded m...
• Re: Getting Reference Index Files In Local Galaxy Install
  Hi, We have a local install of galaxy and I'm trying to add the reference index files for bwa usi...
• Remove "Unpaired" Reads From Quality-Filtered Pared-End Fastq Files.
  Hi there, I obtained two fastq files from GA paired end run. I filtered each file by quality usi...