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• Using DEXSeq count on a sliced bam or sam file
  Using DEXSeq count on a sliced bam or sam file does not seem to run properly. The output file re...
• HISAT2 Output in Galaxy vs Command Line
  In galaxy, I am given a BAM and BAI file. Does galaxy implement the sorting and index function th...
• Help with sorting and merging two biological replicate bam file?
  Does Bowtie2 give, as output, a SORTED bam file ? If it doens't, how could I solve this problem? ...
• cuffdiff does not accept BAM files produced by HISAT2
  I ran HISAT2 on my several  RNAseq samples and then wanted to process the resulting BAMs with cuf...
• Does Tophat Output *.Accepted Hits File Contain Headers?
  Dear All, I want to use the Tophat output files with ".accepted hits" to do analysis outside Gal...
• samtool sort error in sorting BAM files by read name
  Hi, I'm trying to sort my BAM file by read names (-n) on Galaxy but it gives me this error: [bam...
• Recent problems writing Bigwig from Bam files
  I am having problems writing BigWigs using the convert command from an uploaded STAR Bam file. A ...
• how to sort reads by read length
  I would like to sort reads in a bam file by read length. Which tool on the galaxy website can i use?
• Bam to BigWig conversion fail
  I tried converting my sorted bam files to bigwig (my build is mm10) and got this error: 1 is ...
• Need help with "Sort" tool
    Hi Can this tool available on Galaxy be used to sort a sam file before converting to bam file?...
• Error on mapping: my sliced sequence (for a certain gene) gets mapped 3mb away.
  I've sliced my original BAM files to my region of interest, and then transformed the sliced files...
• Impossible to use Htseq-count on BAM files from Tophat2
  Hello, I'm currently facing troubles using galaxy. I want to compare differentially expressed ...
• Hisat2 to cufflinks
  Hi, Recently, I tried use hisat2 to mapping RNA-seq, then use cufflinks to measure the gene expr...
• How Can I Sort Bam/Sam File By Read Names?
  Hi, I need to sort a BAM file by read names, I was wondering if this is possible with a tool inc...