[GenoMax]

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.

[maivantan]

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

[GenoMax]

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?

$ 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

[maivantan]

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

[maivantan]

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

[GenoMax]

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.

$ cd to_directory_with_ref.fa
$ /provide_full_path_to_directory/bwa index ref.fa

[maivantan]

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$

[GenoMax]

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):

$ ./bwa

If that does not work then you may need to make the file executable

$ chmod u+x bwa
$ ./bwa

The second command should produce bwa "help" output. Then you should be ready to run.

[maivantan]

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?

[GenoMax]

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

[maivantan]

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

[GenoMax]

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.

[maivantan]

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

[DavyK]

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.

[TabeaK]

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.