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• Problem in cuffdiff
  Hi everyone...after doing cuffdiff when viewing the data in tabular format of gene differential e...
• 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...
• Trinity run preprocessing
  I am new to Trinity and galaxy instance (https://usegalaxy.org/). I have 17 samples pair ended. I...
• 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...
• Tophat can run negative r
  Regarding to Mean Inner Distance between Mate Pairs, I tried run ~1000000 reads twice: (1) if r...
• Mapping Paired End Reads With Tophat
  Hi all, After mapping, I used IGV to have a look at the mapping. There are a lot of mapped read...
• fastq splitter problem
  fastq splitter is not working on paired end read for some of my file and produce output file with...
• Pre-Processing Of Illumina Rna-Seq Paired End Data
  Hello, I have Illumina 76bp paired end data for a zebrafish RNA-seq experiment and am basically ...
• difference between tophat2 and tophat for illumina
  Hi  I have paired end read and am confused i should tophat 2 or tophat for illumina. What is the...
• Help!! Tophat Paired End Reads
  Hi, I am very confused by my mapping. Please help me figure out what's wrong with my operation. ...
• extract only unique mapped paired end reads
  Hello,  I aligned paired end reads with bwa 0.5.9. Next, I would like to extract only paired end...
• Splitting Biased Paired End FASTQ data
  The FASTQ splitter in Galaxy warns that the tool only works if Paired-end data has equal length r...
• Cufflinks Fpkm
  Hi, I want to use cufflinks handle the results of Tophat. Cufflinks uses FPKM to normalize the e...
• Tophat
  Dear all, This might be a silly question, but I couldn't figure it out by myself :-((. Could you...
• Best Tophat parameters for splicing
  Hey I was wondering if there are any key parameters to consider for Tophat to maximise my chanc...
• Mapped paired-end reads with Bowtie2
  Hi Biostar community, I have paired-end reads for MeDIP-seq. I'm able to mapped read1 and read2 ...
• Tophat "Mean Inner Distance Between Mate Pairs"
  Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in "Mean Inner Distanc...
• Bfast For Solid Paired End Reads
  I am new to RNA-Seq and trying to map ABI SOLID paired-end reads. I've read that BFAST + BWA is ...
• Cuffmerge Question
  I'm new to RNA-Seq analysis and think this question must have been asked before, but I can't find...