[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

[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]

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]

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.