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• 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...
• Bowtie2 problems dataset not available
  Hello! To do mapping using bowtie2, I have a message with "No fastqsanger dataset available". It...
• 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...
• How to extract files out of List of Dataset Pairs
  Hello, I run Bowtie2 with List of Dataset Pairs. Unfortunately, MACS2 (Galaxy Tool Version 2.1.0...
• Multiple fastq files in Bowtie2
  I have 4 lanes in each set of reads. I do understand using the multiple datasets option will run ...
• >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...
• Mapped paired-end reads with Bowtie2
  Hi Biostar community, I have paired-end reads for MeDIP-seq. I'm able to mapped read1 and read2 ...
• How to make Bowtie2 align a specific number of nt
  Hi, I am trying to align some tumor miRNA sequencing data to a viral genome using Bowtie2. In o...
• Failure preparing job-Bowtie2
  Dear Biostars, I hope you are well. While attempting to use Bowtie2, I noticed a "failure prep...
• Galaxy-using trimmomatics with ChIP seq pair ended (only one file with both reads)
  I am trying to run Trimmomatics in Galaxy under "pair end (as collection)" for afastqsanger.gz ...
• (No Subject)
  Hello, I am fairly new to galaxy and I am trying to use bowtie2 to map my reads against a custom...
• using SamToFastq 1.136.0 in Galaxy workflows
  Hello, How can I connect in the workflow SamToFastq and Bowtie2 tools in Galaxy? I am trying to ...
• Unable to fetch the sequence from human genome using start/stop coordinates
  Hello, I am attempting to generate a FASTA from MACS2 generated summits bed file using Galaxy's...
• Paired End FASTQ files
  Hi all, I have a question regarding paired end FASTQ files for chip-seq analysis. Which followi...
• Bowtie 2 output read
  I am using galaxy platform to run Bowtie 2. I have illumina paired end reads (file#1 and file#2)...
• 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...
• TopHat Fata Error: Fusion search fails with Bowtie2, how to try Bowtie1 option? Also truncates file during genome alignment
  I am trying to run TopHat using a GTF annotation to build a transcriptome index, and also search ...
• (Closed) Local Galaxy with grey process
  Hi all, I have a local galaxy installed and today I try submit Bowtie2 process and in my histor...
• Question On Galaxy Reference Genome Window
  Dear Galaxy members, I am new to galaxy and just installed galaxy on aws cloud. I am testing how...
• Web Galaxy Server And Load
  HI, Does anyone know how to check whether the Galaxy server(s) load is really high? My alignment...