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• Bowtie Raw Input
  Hi There Im trying to map RNA-seq data to a reference genome in Galaxy (Main instance) using bot...
• Bowtie on Galaxy - -v or -n ?
  Good morning, I'm using Galaxy with Bowtie for Illumina to map smallRNA sequencing (illumina) on ...
• Metadata error while mapping with bowtie in galaxy
  ChIP seq files sequenced in Sanger / illumina 1.9, when processed for mapping with Bowtie for Ill...
• Accessing S3 Buckets from Galaxy
  I'm trying to access a folder containing fastq files that's located in an S3 bucket from Galaxy. ...
• bowtie2 out of memory
  I'm trying to run bowtie2 in galaxy on my own centos installation to align paired end data to the...
• bowtie2 index file not found by tophat - galaxy cloudman instance error
  Hi, I'm quite new to galaxy, and started after a few tutorials on usegalaxy to launch a cloud i...
• Tophat Error: segment-based junction search failed with err =1
  Hi Everybody, I have this error message when I try to do Top Hat algorithm on my Groomer FASTQ f...
• Running TopHat2 with a GTF file
  Hi everyone,   I am having issues running TopHat 2. I have added the reference genome fasta fil...
• Problem with running tophat2
  Hello everyone, this is the first time i'm trying to run tophat2 on a computer cluster, which a...
• TopHat Dataset generation errors
  Hello I'm trying to use TopHat in public server for alignment my RNA-seq data that generated fro...
• TopHat Error stating that (installed) Bowtie2 is not installed
  I tried to try 'TopHat (v.2.1.0)' locally to align some RNA-Seq data to a reference human genome....
• Tophat And Bowtie2
  Hi, I installed bowtie2 and when running tophat I get the following error: Error in tophat: ...
• Tophat2 index problem
  I'm trying to align RNA-seq data of wheat genome so i used bowtie2 with large index option to bui...
• Tophat Error
  Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isy...
• Tophat Error: Broken Pipe
  Hello everyone, I was trying to run tophat in a local version of galaxy, but I got the following...
• Tophat Error
  Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys...
• Differential Expression in bacteria RNA-seq
  Hello, I got a problem in Cufflinks: I need to analyze fastq file from a RNA-seq (I got bacteria...
• Cufflinks Fpkm
  Hi: I gain the SOLiD sequencing data.I used bowtie to map human genome then I sort the s...
• Bowtie with -a --best --strata does not seem to limit alignments to the best strata
  I am using bowtie for illumina on the NGS Galaxy public server. This is the code for the run tha...
• Error with Bowtie2 mapping against rhesus monkey reference genome
  Hello! I am trying to align a fastq file (fastqsanger) with Bowtie2 against the built-in referenc...
• Tophat Error
  Hi, JUst running a TopHat job which returned the following error: Executing: /gpfs/cluster/isys...