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• 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...
• combining indexed paired reads from two lanes of a Hiseq rapidrun
  Hi I am doing paired end RNAseq, I have a single multiplexed pool that was run over both lanes o...
• Trimming And Thinning Of Paired-End Reads
  Hi galaxy users, I've been experiencing some problems trimming the adapters and filtering by qua...
• Analysis of forward and reverse reads
  Hello. Newbie here: I have recently done some chip-seq, and for each sample, I have different ...
• 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...
• 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...
• 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...
• --fr versus --rf option in Hisat2
  Hi! We have a library of paired reads generated by the UTF-8'en-us'SMARTer Stranded Total RNA-Se...
• Kraken (assign taxonomic label...)
  One Illumina file fastq.gz contain all info about paired-end reads. I used by usegalaxy interface...
• Tophat Paired End Read
  Hi all, I have paired end RNA-Seq reads ( Illumina Hiseq 2000) in seperate files. Before mapping...
• 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...
• 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...
• my tool and collections
  Hello, I want to do something related to writing my own tool (in perl) and 'collections'. I have...
• 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...
• chip-seq analysis using galaxy
  For paired-end analysis, why do i see Chip-Seq Tag file 1 and 2. ? Both forward and Reverse reads...
• 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...
• Separating (F and R) reads uploaded from NCBI SRA & mapping them using BWA-MEM
  Can someone explain to me the best way to prepare NCBI SRA data for subsequent mapping to a cust...
• 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 ...