• TopHat2 number of mapped reads?

    Hello

    I am new in RNA-seq. I am using Tophat2 to map single end reads to mm9. I am using tophat2...

  • TopHat --max-multihits interpretation

    Hello,

    I have read some postshere regarding TopHat's --max-multihits option, where and option of...

  • New Tophat Adds Multimappers As Entirely New Reads

    What are the benefits/disadvantages of allowing multi-hits in tophat ?

    Since tophat2.0 the defau...

  • Cufflinks run showing “Multihit not found”

    I run my RNA seq data for alignment and assembly with the below mentioned options. The cufflinks ...

  • Removing fused transcripts from RNA seq data

    Hello!
    I have performed alignment of paired-end data with tophat with the following options:

    ...

  • Tophat Both Pairs Must Map Concordantly

    Hi,

    I have run tophat with the following parameters, specifying each reads can only map once and...

  • tophat --max-multihits impacts 'mapped in a proper pair'

    Hi everyone,

    I have a RNA-seq library (paired-end) with a large amount of multimappers because i...

  • How to remove non-unique mapping reads with Hisat?

    Is there an option in Hisat that is similar to g/--max-multihits in Tophat? I can not find it in ...

  • How to get unique mapped reads?

    Dear all,

    Previously I thought when the -g/--max-multihits option in tophat was set to 1, then I...

  • error while running tophat ReadStream::getRead() called with out-of-order id#!

    Hello All
    I am running tophat v2.1.1 on human sample pairend reads (6.0 gb data)
    after running fo...

  • tophat reporting output problem

    Hi

    I new to rna seq analysis, i have reference genome and tried to map reads. After running Toph...

  • Selecting best RNA-seq mapping with TopHat

    After mapping my PE RNA-seq with Tophat with three different options (given below). I found the f...

  • How can we plot alignment distribution ?

    I am looking at figure [8G][1] in this article journals.plos.org/plospathogens/article?id=...

  • Error RNA-seq data, TOPHAT

    Hi All,

    I tried aligning the RNA-seq reads to the genome using tophat, used the following comman...

  • Multiple alignements tophat

    Hello everyone. I'M analyzing transposons and repetitive elements that are expressed in some tiss...



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