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  • #31
    Thank you Cytosine, that did it !!!

    I had tried adding those two parameters from another thread I had seen before I registered with SEQanswers, (but not the same thread that you have directed me to).

    As I said before, when something does not work I tend to remove it again rather that clog up a file with apparently non-working parts.

    This is what I now get:-

    $ ./samtools.exe

    Program: samtools (Tools for alignments in the SAM format)
    Version: 0.1.19-44428cd

    Usage: samtools <command> [options]

    Command: view SAM<->BAM conversion
    sort sort alignment file
    mpileup multi-way pileup
    depth compute the depth
    faidx index/extract FASTA
    index index alignment
    idxstats BAM index stats (r595 or later)
    fixmate fix mate information
    flagstat simple stats
    calmd recalculate MD/NM tags and '=' bases
    merge merge sorted alignments
    rmdup remove PCR duplicates
    reheader replace BAM header
    cat concatenate BAMs
    bedcov read depth per BED region
    targetcut cut fosmid regions (for fosmid pool only)
    phase phase heterozygotes
    bamshuf shuffle and group alignments by name

    Thank you so much for leading me by the hand ... now I might be able to get on with my DNA analysis of my BAM files.

    Dennis Wright


    • #32
      Hi all,

      From my experience Cygwin will be a continuous pain in the rear when trying to get new programs to compile. Unless this is really the only thing you can imagine having to compile, I would recommend buying another HD and installing a linux distribution. Because Cygwin is light weight, it is missing a ton of standard libraries. Since a lot of programs have dependencies that are met with standard Linux distros they are just not listed. What ended up happening for me was i tried $ make, found the compiler complaint, then installed Cygwin library and rinse and repeat for many iterations.

      One pretty good newbie solution/stepping stone is Bio-Linux, which is based on Ubuntu (the window user friendly Linux distro). It comes with a ton of useful software preinstalled along with all their dependencies (obviously). These same packages are used for a ton of programs, so in the end much less time sifting through $ make outputs all day
      It has been well worth the investment in the linux learning curve.

      Bio-linux site:
      --Please take everything thing I say with a grain of salt, because, if grad school has taught me anything, it's that I'm an idiot--


      • #33
        Thank you BurlEarl for your suggestion but I have no need, or desire to dive in deeper into Unix/Linux.

        I taught myself Microsoft Basic in 1980 and have had a computer at home since then. At that time I taught myself and wrote programs in Z80 machine language. But I have not had a need to learn C+, C++, Perl, Ruby or any of the other languages. In recent times I have confined myself to HTML and CSS to build and maintain my website and at 70 can't be bothered in learning more that I have to!

        While I haven't bothered to work out the intricacies of PATHs, SOURCEs and ENVIRONMENTs I am now able to drop a .bam file into the Samtools-0.1.19 folder, open the Cygwin Terminal window, cd to /samtools-0.1.19 directory and on issuing the command:-
        ./samtools.exe index xxxx.bam
        after a short delay, the xxxx.bam.bai index file appears in the samtools-0.1.19 directory.

        I can then use IGV 2.3.34 (Intergrative Genomics Viewer) to analyse the DNA results emanating from Next Generation Sequencing of the Y Chromosome.

        That was all I needed Samtools to do for me so thanks to SEQanswers for assisting me to that end.
        Last edited by Scorpion43; 08-04-2014, 05:04 PM. Reason: Spelling


        • #34
          Well you are certainly more qualified than me! I just started this bioinformatics journey (hence all the newbie info). Glad it's working for you. Good luck with analysis and whatnot.

          --Please take everything thing I say with a grain of salt, because, if grad school has taught me anything, it's that I'm an idiot--


          • #35
            A more functional alternative to cygwin would be bio-linux (ubuntu with many programs such as samtools pre installed) in a virtual box.


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