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  • GenoMax
    replied
    If you can use the "oryza sativa japonica" genome then pre-built indexes for bwa and bowtie2 can be downloaded from the Illumina igenomes page: http://support.illumina.com/sequenci...e/igenome.ilmn

    If you are working with a different genome then you will need to download and build the index yourself from the genome fasta file.

    A fair warning. Your laptop only has 4 GB of RAM so something like rice genome may be difficult to handle (creation of indexes/alignments) on your macbook.

    Leave a comment:


  • maivantan
    replied
    Here the result:

    USER-no-MacBook-Pro-4:~ user$ ls -l /Users/user/tan_analysis/bowtie2-2.1.0/example/index/
    total 16512
    -rw-r--r--@ 1 user staff 4210730 2 20 2013 lambda_virus.1.bt2
    -rw-r--r--@ 1 user staff 1520 2 20 2013 lambda_virus.2.bt2
    -rw-r--r--@ 1 user staff 17 2 20 2013 lambda_virus.3.bt2
    -rw-r--r--@ 1 user staff 12126 2 20 2013 lambda_virus.4.bt2
    -rw-r--r--@ 1 user staff 4210730 2 20 2013 lambda_virus.rev.1.bt2
    -rw-r--r--@ 1 user staff 1520 2 20 2013 lambda_virus.rev.2.bt2

    I want to analyze my file in rice. Now i try to practice the lambda file first.
    If i want to analyze for rice, which reference for index should i use

    Thank you very much

    Leave a comment:


  • GenoMax
    replied
    Looks like you switched to using bowtie2 (instead of bwa)? I assume you are following the Bowtie2 example here: http://bowtie-bio.sourceforge.net/bo...-phage-example

    It looks like you have built the index for the lamba genome but let us make sure. Genome index files (there are several) are used for the mapping. "bowtie2" is the program that does the alignments.

    Can you post the output of following command?
    Code:
    $ ls -l /Users/user/tan_analysis/bowtie2-2.1.0/example/index/
    See the section under "Aligning example reads" to actually run the alignment: http://bowtie-bio.sourceforge.net/bo...-phage-example

    Leave a comment:


  • maivantan
    replied
    Dear GenoMax
    I did as your instruction. how ever, when i typed a command as
    USER-no-MacBook-Pro-4:index user$ /Users/user/tan_analysis/bowtie2-2.1.0/example/index/lambda_virus.1.bt2 lambda_virus.1.bt2
    -bash: /Users/user/tan_analysis/bowtie2-2.1.0/example/index/lambda_virus.1.bt2: Permission denied

    How can i do with permission denied.
    i did chmod u+x hello.sh
    but i got

    USER-no-MacBook-Pro-4:~ user$ chmod u+x hello.sh
    chmod: hello.sh: No such file or directory

    Can you tell me how is it?
    Thank you

    Leave a comment:


  • maivantan
    replied
    Thank yu GenoMax very much.
    I am going to learn it

    Leave a comment:


  • GenoMax
    replied
    Originally posted by maivantan View Post
    USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$ ./bwa index ref.fa
    [bwa_index] fail to open file 'ref.fa' : No such file or directory
    It would be useful to invest a day in learning UNIX essentials. A very useful resource for biologists to learn UNIX (I assume you are one) can be found at this link: http://korflab.ucdavis.edu/Unix_and_...1.1.html#part1

    As for your specific problem. Your ref.fa (fasta reference file) does not appear to be in the same directory as the bwa program. I have highlighted the error in red above.

    Best option is to change to the directory where the ref.fa file is present. Then run the bwa command providing full path to the bwa executable.
    Code:
    $ cd to_directory_with_ref.fa
    $ /provide_full_path_to_directory/bwa index ref.fa

    Leave a comment:


  • maivantan
    replied
    Dear GenoMax,
    I am sorry to disturb you, but I got the problem here:
    when try to index the reference as the following, its fail. Would you please help me
    Thank you very much

    USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$ ./bwa index ref.fa
    [bwa_index] fail to open file 'ref.fa' : No such file or directory
    USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$ ./bwa mem ref.fa reads.fq > aln-se.sam
    [E::bwa_idx_load] fail to locate the index files
    USER-no-MacBook-Pro-4:bwa-0.7-1.5a user$

    Leave a comment:


  • GenoMax
    replied
    Are you able to see the executable file (should be called bwa)? You can verify that it is executable by trying to run it like this (assuming that you are in the bwa directory):

    Code:
    $ ./bwa
    If that does not work then you may need to make the file executable

    Code:
    $ chmod u+x bwa
    $ ./bwa
    The second command should produce bwa "help" output. Then you should be ready to run.

    Leave a comment:


  • maivantan
    replied
    Dear GenoMax,
    I am using matchbook pro v10.7.5, ram 4gb, core i7.
    i did down load from the web site and make it in terminal.
    Do you have any suggestion?

    Leave a comment:


  • GenoMax
    replied
    How familiar are you with unix? Did you download/compile bwa from sourceforge?

    Leave a comment:


  • maivantan
    replied
    Thank you GenoMax,
    but when i type bra index ref.fa
    error is command not found.
    Do you have any suggestion?

    Leave a comment:


  • GenoMax
    replied
    Originally posted by maivantan View Post
    I do not know the command to run fasta file in bwa
    Anyone can help me?
    Thanks very much
    Maivantan: You have probably looked at the bwa manual already. http://bio-bwa.sourceforge.net/bwa.shtml Main commands are in the synopsis.

    bwa will accept fasta files in place of fastq (*.fq) files on those commands.

    Leave a comment:


  • maivantan
    replied
    I do not know the command to run fasta file in bwa
    Anyone can help me?
    Thanks very much

    Leave a comment:


  • DavyK
    replied
    Originally posted by TabeaK View Post
    I realise I never got back on this thread: I have also not had any decent alignments using BWA 0.6.x. I since downgraded to 0.5.x and everything is running well.
    Yeah I might try using a 0.5.x version and compare the alignments to see if the upgrade is worth it.

    Leave a comment:


  • TabeaK
    replied
    I realise I never got back on this thread: I have also not had any decent alignments using BWA 0.6.x. I since downgraded to 0.5.x and everything is running well.

    Leave a comment:

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