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  Hi All, I have some paired end stranded RNAseq data prepared using an Illumina TruSeq Stranded m...
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• ChIP-seq mapping with Bowtie for Illumina 1.1.2
  Hi, I mapped my chip seq data with 'Map with Bowtie for Illumina 1.1.2' and used 'Filter SAM or ...
• Problem with Filter SAM or BAM, output SAM or BAM files on FLAG MAPQ RG LN or by region (Galaxy Version 1.1.1)
  First i don't know if this is the correct place to report tool problem. I did not get any bug dat...
• Extracting Reads Mapped From Bwa Mapping
  Hello, I recently figured out how to filter the output bwa SAM file for flag type in order to de...
• Metadata galaxy error
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• Cannot set metadata on .bcf output from mpileup
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• Sam Filtering And Header/Sorting Issues
  Dear All, I would like to add some filtering steps in my RNA-Seq pipeline. To do so, I used the a...
• AddOrReplaceReadGroups errors with BWA-MEM input
  Hello, I appreciate if someone can help me figure out why I get this error. Could not displ...
• How do I obtain uniquely mappable reads from bowtie on galaxy?
  Hello, I'm using bowtie on Galaxy to map my RNA-seq reads to the sacCer2 yeast ref genome. I was...
• Re: Ngs Mapping Using Lastz
  Hi, I'm trying to map a data set containing 454 reads to a reference genome using LASTZ alignmen...
• Convert SAM to sorted BAM
  I am looking for a tool to convert SAM to sorted BAM (sorted by the coordinates, such as with sam...