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• Use Own Junctions Or Not
  Dear All, I want to compare the pre-mRNA alternaive splicing events between RNA- seq datasets. S...
• intron retention analysis
  Hi! I am hoping to use the analysis tools that are available in Galaxy to achieve my tasks. I am ...
• RNA-star: splice junction
  Hello, I am new to RNA-seq data. I am using the built-in index and using the reference genome wi...
• tophat on galaxy
  I have run a RNA-seq data set on top hat, Groom file, i have got error, i dont have any idea how ...
• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• Are Reads Of 36Nt In Length Long Enough To Accutatly Map On Splicing Junctions?
  Hi All, I have a very basic question. I have RNA-seq datasets of several cell types and want to ...
• Tophat Output Spice Junction Output
  Hi, where can I find an explanation of the columns in the splice junctions output? From 7 to12 th...
• Where is "Tophat for illumina Find splice junctions"?
  Dear Sir/Madam: This is Bob. I am interested in the course of RNA-seq-analysis-mapping. The demo...
• How can I improve my mapping alignment rate with MiSeq 2x300 bp paired-end reads?
  Edit 1: it appears I have misinterpreted the raw data, which in turn led to my poor results. The ...
• 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...
• cufflink only assembles 1 transcript for gene of interest when tophat splice junctions suggest different alternative splicings
  Hello Friends I am currently doing RNA-seq hoping to find new transcript (we found with our qPC...
• Tophat job not running
  Dear sir, my top hat job not running. My data were showing some exclamatory sign after running t...
• Inbuilt reference genome
  Hi, I ran a top hat analysis on samples, but after the cuffdiff step, I do not have any genes an...
• Re: [Galaxy-Dev] Tophat Output
  Hello Jianpeng, The numbers 87 and 93 are the actual maximum lengths of the aligned regions on e...
• Should I "Use Raw Junction" And "Only Look For Supplied Junctions"
  Dear All, I have two more questions about settings for Tophat. My aim is to look for the deffer...
• cuffdiff outpuit interpretation, splicing and promoter differntial expression
  dear all i have read many posts but still unable to understand that in cuffdiff output what does...
• Extract depth coverage of a particular region from BAM file
  Hi, If any kind soul could help, I loaded BAM files in IGV and i notice some interesting splicin...
• Cuffdiff input into Cummerbund error?
  Hi all, So I completed a standard workflow using top hat through cuffdiff in order to find diffe...