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• top hat splice junction
  hi i am working on ngs data and used tophat for aligning the sra data to refernce genome. top ha...
• 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...
• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• Galaxy Tracker Browser Freezes When Zoomed In
  Hi, I'm going through the RNA-seq exercise at http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-se...
• Re: Galaxy'S Tophat 2 -Gtf Option
  Hi Zain, Annotations are used with Tophat2 the same way that they are with Tophat. Open up the ...
• Use Own Junctions Or Not
  Dear All, I want to compare the pre-mRNA alternaive splicing events between RNA- seq datasets. S...
• Cuffcompare successful but generate empty files.
  Hello friends I am currently doing RNA-seq for 3 datasets (obtained publicly through NCBI-SRA...
• Re: [Galaxy-Dev] Tophat Output
  Hello Jianpeng, The numbers 87 and 93 are the actual maximum lengths of the aligned regions on e...
• Error "Out Of Memory" When Trying To Retrieve Output
  Hello, I wanted to download the accepted junction .bam file from tophat output of my local instan...
• 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...
• 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...
• "View Details" Of Tophat Alignment
  Hi All, After I finshed Tophat alignment for RNA-seq, I took look at the details of parameters b...
• Please Help Me Check The Quality Of The Tophat Mapping To Reference Genome
  Dear All, I ran "Flagstat" under "NGS: SAM Tools" to check the quality of the Tophat output (the...
• Error using stringtie - AttributeError: 'NoneType' object has no attribute"
  Hi, I have **RNA-seq data** and I am interested in whole gene expression results but also transcr...
• Re: [Galaxy-Bugs] Cdna Mapping 454
  Hi Chris, I'm cc'ing galaxy-user because your questions are more about use than bugs. You're c...
• 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...
• 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...