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• 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...
• Analysis of forward and reverse reads
  Hello. Newbie here: I have recently done some chip-seq, and for each sample, I have different ...
• 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 ...
• 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...
• Using Files Produced By "Barcode Splitter"
  I used the "Barcode Splitter" tool to split multiplexed RNA-Seq libraries into separate files. I ...
• Fastq Quality Trimmer For Pe Illumina?
  Hello, I was wondering, can Galaxy's FASTQ Quality Trimmer tool be used on Illumina paired-end d...
• Issue With Saving 'Manipulate Fastq' In Workflow; And Request For Advice Dealing With Barcoded 454 Data
  Hi, I'm a new user, learning how to use Galaxy while I wait for my 454 results. So I'm not actua...
• Cannot select data sets in local galaxy sever
  Hey, So I've installed a local galaxy server in order to helpout processing some large data we h...
• 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...
• Forward and Reverse reads from paired end sequencing
  The fastq dataset we have after illumina whole genome sequencing is in the form of two files - fo...
• 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...
• 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...
• Making paired-end reads the same length
  I have paired-end data (in two separate files).  I have groomed my files, and would like to filte...
• >90% aligned concordantly 0 times ChIP-seq Bowtie2
  Hi, I know this question have raised many times here and in other forums but I've tried everythi...
• FASTQ file split (forward and reverse not of same length)
  Is there a Galaxy package which will split a previously joined fastq which will have unequal forw...
• Extract reads in FASTQ/A format from NCBI SRA
  Hi. I downloaded an SRA accession. In the results, the spots were separated but is in the same fi...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...