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• How to get only paired end or single end uniquely mapped reads with Bowtie2?
  Hello, I am using bowtie2 on galaxy to map ChIP-seq single end and paired end libraries to a ref...
• Problems running Bowtie2!
  Hi everyone, I'm trying to map a paired-end seq. to the human genome using Bowtie2. Unfortunately...
• Bowtie2
  Hi All I'm trying to use bowtie2 in Galaxy but though I have uploaded a valid pair of fastq file...
• Bowtie2/Samtools files are not visualized with Trackster: Fatal error Exit code 255 ()
  I am trying to map 8 paired-end reads on to the same reference custom-build genome. Each of these...
• Low mapping of paired-end reads with tophat2
  Hello. I'm trying to map paired-end reads on reference scaffold using tophat2. But the percentage...
• bowtie2 output only mapped reads --no-unal option
  Hi, I've been trying to run the galaxy bowtie2 tool and couldn't find an option to report only a...
• How to check unaligned reads?
  I have a pair end SRA files for which I have done FASTQc. The SRA files are then mapped against ...
• 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...
• Bfast For Solid Paired End Reads
  I am new to RNA-Seq and trying to map ABI SOLID paired-end reads. I've read that BFAST + BWA is ...
• Help! I'm using trimmomatic in Galaxy, but it doesn't recognize a part of input dataset.
  I'm using Trimmomatic to trimming paired end reads. When I set "Single-end or paired-end reads?"...
• Mapping paired reads to reference genome, variant calling
  I am trying to map a trio of paired-end Illumina reads to a reference genome, then identify polym...
• Paired-end insert size upper limit
  I am mapping paired-end reads using Bowtie2 and setting "maximum insert size for valid paired-end...
• RNA seq beginner
  I just got back RNA seq data produced on the HiSeq 4000. They prepared the libraries and performe...
• Analysing paired end RNAseq data with poor quality score
  Hello, I'm new in NGS and i'm currently working on RNA-seq. I had 6G of illumina reads and proce...
• Fastq Joiner
  Hi all, Has anyone used FASTQ joiner with a file containing multi-mapped reads? I'm pretty sure ...
• RNAseq data to be processed in two ways: (i) mapping to de novo Trinity-based transcriptome and (ii) mapping a relatively new genome
  Hello all, I am new to RNAseq data and learning this process step by step, so I have a few quest...
• Help!! Tophat Paired End Reads
  Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. ...
• Use paired collection on wrapper
  Hi, I'm try to write a wrapper for a tool that performed subsampling of fastq file. The script i...
• Converting pair-end dataset to fastq
  I'm new to galaxy and am trying to use the cloudmap workflow to conduct "Hawaiian variant mapping...
• Can a genome that's been released be added so I can map against it
  Hi there, I will be mapping my RNAseq reads to a genome of interests soon. Mapping with Bowtie2 ...
• Bowtie 2 output read
  I am using galaxy platform to run Bowtie 2. I have illumina paired end reads (file#1 and file#2)...
• bowtie2 rename dataset from paired list
  Hi, I have a paired reads dataset list that I use for a bowtie2 workflow. I try to rename the ou...