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  • New to RNAseq

    Hello
    I am new to RNAseq analysis.
    Jut got my sequences and I want to start.
    I want to allign the reads to reference transcriptome.
    Any guidelines or help for a beginner.

  • #2
    Maybe you could begin with trying some align softwares, such as BWA

    Comment


    • #3
      Watch some tutorial videos at Galaxy:
      Galaxy is a community-driven web-based analysis platform for life science research.

      Or, if you're comfortable with the command line, jump right in with something like Tophat.

      Comment


      • #4
        There is a tutorial for the analysis of RNA-seq data:
        Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

        Comment


        • #5
          Thank you very much.
          It helped a lot.
          Next I wanted to do is "to identify polymorphisms in arabidopsis genome" and I have paired end DNA sequences. any hint about where to start?

          Comment


          • #6
            The two main programs people use for SNP detection are samtools and GATK. I'd start with reading the manuals for those.

            Comment

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