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  • introducing BAMseek, a large file viewer for BAM and SAM

    Hi SeqAnswers community,

    I have been a long time follower of SeqAnswers but have just joined and would like to make available a tool I have been working on called BAMseek.

    BAMseek is a large file viewer for browsing BAM and SAM alignment files. BAMseek offers a graphical interface to viewing SAM/BAM files and allows you to jump around to random locations in your files.

    I currently have a Mac OS X Snow Leopard build available at http://code.google.com/p/bamseek/ If people find this useful, I can also make a Windows executable available.

    This is the first release of BAMseek, so any suggestions/feedback/questions are welcomed. I will do my best to reply and incorporate feedback.

    thanks!

  • #2
    Does it have the ability to non-interactively generate "snapshots" of a given region of the fly? Im looking for this in an open source tool.

    Comment


    • #3
      I found it easy to install, and it is a very clean interface.

      Comment


      • #4
        Originally posted by zee View Post
        Does it have the ability to non-interactively generate "snapshots" of a given region of the fly? Im looking for this in an open source tool.
        Hi zee,
        I don't know if I quite understand what you mean. I could add the ability for the user to select a few rows and do a Copy of the selected data (in fact, I think that would be nice for the next version). If you are looking to automatically extract all the reads in a certain genomic region, I would suggest the "samtools view" command in the samtools software (which requires the file to be sorted and indexed). For BAMseek, I decided to not require the file to be sorted in order to browse it.

        Does that help at all?

        Comment


        • #5
          Can you summarize how BAMseek compares to other BAM viewers like Bambino and BamView? What are it's relative strengths?

          Thanks

          Comment


          • #6
            Originally posted by tnabtaf View Post
            Can you summarize how BAMseek compares to other BAM viewers like Bambino and BamView? What are it's relative strengths?

            Thanks
            Sure. I am aware of the tools you mentioned, but I have not used them too much myself, so please correct me if I am wrong. It looks like those types of programs are for visualizing alignments on the genome, which is a very useful way for exploring your data. BAMseek gives you a different view of the data - it allows you to view the file itself, which to my knowledge, could only be done if you are familiar with command line operations. Typical text editors cannot view SAM/BAM files because the files are large (too much to put into memory at once), and BAM files are not in a human-readable form. BAMseek could be useful if you just wanted to open up the file and get a feel for the type of data it contains - is it paired-end? does it contain auxiliary flags? what's the read length? ...

            So in short, I see these as complimentary tools that allow you to explore those very large BAM/SAM files.

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            • #7
              OK I had a look at Bamseek and I thought it would be another alignment graphical viewer. It definitely does not suit my purposes as I am already quite experienced with the samtools and Picard utilities. Nice for the GUI people though.

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              • #8
                BAMseek - now on Windows

                Cross-platform version of BAMseek now available at

                http://code.google.com/p/bamseek/

                BAMseek is a file viewer that allows you to browse through BAM and SAM files with a friendly user interface. I recently uploaded a cross-platform version (BAMseek2011June01.jar ) that can run on both Windows and Mac (and anywhere java runtime 1.6 is installed). To run, simply download and double click the .jar file. I would still consider this in its testing stage, so keep that feedback coming! Thanks.

                Comment


                • #9
                  How different is it from IGC and TVIEW ? I know IGV changes the BAM alignment of my reads to reference , and so I have discontinued using it. I hope BAMseek does not do the same.

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                  • #10
                    BAMseek is a text viewer that lets you see the actual text within a BAM file (such as what you would get with samtools view). So probably not what you are looking for if you are looking for a new alignment viewer. What do you mean that IGV changes the BAM alignments to reference? I haven't noticed IGV changing the data.

                    Justin

                    Comment


                    • #11
                      Hi,

                      I have tried BAMSeek and like the way it gives individual reads; however, it seems that is all there is. Is there a "search/find" function if I wanted to look for a specific sequence. Or is there a freely available tool for this?

                      Thanks,
                      Marija

                      Comment


                      • #12
                        Originally posted by madebeljak View Post
                        Hi,

                        I have tried BAMSeek and like the way it gives individual reads; however, it seems that is all there is. Is there a "search/find" function if I wanted to look for a specific sequence. Or is there a freely available tool for this?

                        Thanks,
                        Marija
                        You are correct, there isn't a search/find function available. To do that, there is a lot of power and flexibility from using samtools and grep in the command line. You might try something like this

                        Code:
                        samtools view -h input.bam | grep TCTGACTCTGTGTA
                        You can get fancy and limit your search to particular columns (using something like awk) or allow for mismatches in the sequence using wildcards. So I would suggest that route. Hope that helps.

                        Justin

                        Comment

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