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• parameters and library type for tophat
  hi i haev SRA ids on which i am working. i plan to generate a reference based assembly. 1. i ha...
• How to split a merge piared data using ncbi SRA tools?
  can I split a merged paired end extract reads into two separate data (acc. to their ends) using n...
• what type of library to choose in set advanced cufflink option
  hi i have performed QC then groomer then tophat on SRA sequences which were single end. now i wa...
• How to unzip the fastq files to be used in Tophat?
  While I export RNAseq data from EBI SRA database. It came in xxx.fastq.qz format, which are not a...
• Cufflinks Fpkm
  Hi, I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the e...
• top hat splice junction
  hi i am working on ngs data and used tophat for aligning the sra data to refernce genome. top ha...
• sra dataset in galaxy
  how to make sra dataset in galaxy for analysis.please help me i am highly confused how to use it....
• sra data assembly
  hi i want to know tools to be used for SRA data assembly. i plant ot use data from ncbi sra.
• Need Help To Split Paired-End Dataset
  I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial...
• (No Subject)
  I am new to the NGS analysis. I need help to solve this problem. As shown in my previous emial...
• Help with downloading files from EBI SRA
  I am new to galaxy and have been trying to figure out how to align RNA-seq reads to a genome in o...
• analysis of tophat results
  hi i have done qc and then groomed single end sra sequences from ebi. i ran tophat. i am getting...
• Markduplicate single end reads miRNA seq data
  I am trying to analyze a RNA seq, single end SRA dataset. For this do i have to perform Markdupli...
• TopHat splice junctions
  Dear all, I'm trying to detect alternative splicing events from RNA-seq experiments. I have used...
• Can I Convert Paired-End Datasets Into Single End Ones?
  Dear All, I have some paired-end datasets to be analyzed, but I am not sure about their Mean Inn...
• Decompression of sra files and further analysis
  Case: 05508803 Dear Jen, Thanks that you are trying to help me. How can I uncompress the thre...
• TopHat alignment of RNA seq data
  Hello everyone, I want to use TopHat trough Galaxy to perform the alignment of single end RNA Se...
• EBI SRA Data Import
  Hi guys i have just imported these datasets into Galaxy in fastq format http://www.ncbi.nlm.nih...
• fastq joiner and tophat
  Hi,   I have paired end reads of two samples and i used FASTQ joiner to join them, now i want t...
• Which "Library Type" Should I Use For Single-End Reads
  Hi All, I have a very basic question about parameters for running TopHat. I have datasets of si...