Fasta file for Step 1

[John G]

Hi,

I successfully ran the non-space version of CLARK with your help. I am planning to now run it in --spaced mode. I am attempting to run the second step (Step 1), in which you run classify on the fasta file. Herein lies my question. I used your set_targets script for my original CLARK runs with bacteria and virus dbs at species level, which downloaded all the fna's for each bug into a separate folder for each fna. Can I somehow use the fasta files that your set_targets downloaded for input into classify at Step 1 (see below for step i am attempting to initiate)? Or am I completely interpreting the instructions incorrectly and am heading down the wrong path?

Step 1: Create the discriminative 31-mers of the database you have defined in step 0 (if they do not exist already). This can be done by running the default variant CLARK on the sample of your choice, for example: 
$ ./classify_metagenome.sh -O sample.fa -R result

Thanks,

John

[Rachid OUNIT]

Hello John,

Yes, you are in the right track, you can use any fastq/fasta file "of your choice". 

You can create an empty/dummy file if you want.

Best,

Rachid 

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[John G]

What do you mean by "create an empty/dummy file"? I know how to create one, but you saying an empty fasta file? So is this step not necessary?

[Rachid OUNIT]

As indicated, this step is needed only if you have not built the database of specific 31-mers.

Best,

Rachid 

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[John G]

That makes sense, but to my original question asked in a different way. When I ran set_targets and it downloaded the info from ncbi for bacteria/viruses, did your script also build the 31 mers? If not, where is the fasta file that I need for generating the 31 mers?

[Rachid OUNIT]

First, the reference sequences for the database are first downloaded. Second, the database of specific k-mers is built. That's why there is two different scripts.

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[John Gillece]

I understand that. So when I run the second script to generate the specific k-mers as defined in step 1 of the CLARK-S section (run $ ./classify_metagenome.sh -O sample.fa -R result), where do I point the -O given that I've downloaded the bacteria/viruses with your set_targets.sh?

John

[Rachid]

Hi John,

You point to the address of your file (any file you want for that step). The database you downloaded are stored in the folder you indicated with "set_targets.sh" (you can find the addresses of the database sequences in the file "targets.txt" in that directory).

Let me know if there is another matter otherwise, is it okay to mark complete this topic ?

Cheers,

Rachid

[John Gillece]

Hi Rachid,

Thanks! You can mark it as complete. I may have follow up questions, but can start a new thread.

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