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  • Genome Browser to visualize RNA-Seq Data

    Hey there,

    I am looking for a Genome Browser that is able to visualize my Helicos sequencing data (BAM-files) on the Arabidopsis transcriptome (TAIR10) and additionally having the possibility to export the number of reads aligned to each gene into a text or excel file.

    Up till now I tried Integrated genome browser and Integrative genomics viewer. But they do not seem to have this feature.

    If somebody knows a good one pls tell me

  • #2
    Artemis is able visualize. Not sure about the exports. See http://www.sanger.ac.uk/resources/software/artemis/

    Best regards,

    Peter

    Comment


    • #3
      Originally posted by Dolphin22 View Post
      Hey there,

      I am looking for a Genome Browser that is able to visualize my Helicos sequencing data (BAM-files) on the Arabidopsis transcriptome (TAIR10) and additionally having the possibility to export the number of reads aligned to each gene into a text or excel file.

      Up till now I tried Integrated genome browser and Integrative genomics viewer. But they do not seem to have this feature.

      If somebody knows a good one pls tell me
      I would recommend skipping a browser for this step and use HTSeq-count or BEDTools. I generally consider HTSeq-count the easier of the two as you don't have to bother with everything being in BED format and can work with a SAM and GTF/GFF file.

      Comment


      • #4
        @chadn737 Sounds good thanks for the advice!!

        Do you a source where I can download a binary fo HTSeq for Windows? I was looking at http://pypi.python.org/pypi/HTSeq but I could not find a binary.

        Googeling also did not retrieve anaything

        Comment


        • #5
          There isn't a binary. It is part of a package of python scripts. You will need to have python and the necessary prerequisites.

          Comment

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