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  • Bowtie2 basic problem!

    Hi

    I'm new in the bioinformatic field and I have a basic problem

    I have a read,in fastq format, ready to align on my reference genome (human genome), but I'm not able to do that!

    I've understand that I must to indexing my genome and create a basename before convert my fastq in a sam file.

    I need your help, I've read the tutorial but I haven't the sufficient bioinformatic knoledge to do that by myself.

    Thanks

  • #2
    Look at the 'Getting started' section of the Bowtie webpage and work through their example.

    You can also download pre-built versions of the genome index from the links on the Bowtie webpage, including links to Illumina's iGenomes.

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    • #3
      Solved, thanks!

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      • #4
        Hi,
        i'm trying to index GRCh37 with Bowtie2. RAM is 1.5Gb and indexing has been ongoing for more than 48 hours.
        Is it normal?

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        • #5
          No, Bowtie2's indexing is really slow, but not THAT slow. When you say "RAM is 1.5Gb" do you mean the amount of RAM used by the process, or total memory on the computer? Also, knowing the exact operating system and CPU type would be very helpful.

          Also look at the CPU utilization for that process (e.g. with "top").

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          • #6
            The total memory of computer is 4Gb while 1.5Gb is the memory allocated for ubuntu that I use as virtual machine. What do you intend for CPU type. Processor is i3, 1.8Ghz.
            Is "top" a command that I have to digit?
            Now indexing is running, so I can't work on shell!!

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            • #7
              I don't think 1.5Gb is enough for Bowtie2 to index or map to Human. If you have a 64-bit OS, you should kill the process, give Ubuntu all the memory, and restart it.

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              • #8
                1.5GB RAM is not enough for this process (or the VM). Plus you are probably running 32-bit Ubuntu, which will become a problem with human genome size datasets. You should find an alternate machine with better hardware to do this.

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                • #9
                  No I'm running 64-bit Ubuntu. So do you think I might solve this problem allocating the entire RAM to Ubuntu virtual machine?

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                  • #10
                    How much actual RAM do you have (4?) on this machine? Since the host OS is using some of it you will not be able to allocate all 4GB for the VM.

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                    • #11
                      On my PC I have 4Gb of RAM. I suppose it could not be possible to allocate all 4Gb for VM. What can I do to improve performance of my PC?

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                      • #12
                        Maybe I could expand RAM of my PC. What do you think about it?

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                        • #13
                          Are you able to purchase more RAM? Please be aware that trying to do human data alignments in a VM is going to be a difficult task. You may be able to run a single alignment thread in the VM.

                          From Bowtie Manual

                          Bowtie 2 indexes the genome with an FM Index (based on the Burrows-Wheeler Transform or BWT) to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 gigabytes of RAM.

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                          • #14
                            Or I could allocate 3Gb of RAM for VM? It could improve indexing and other analyses?

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                            • #15
                              I have a Mac with 4GB of RAM and 1333Mhz. It is my personal machine but do you think I could use this computer to run analysis or Mac is not good?
                              Excuse me but I'm a newbie.

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