Bowtie2 Indexer (bowtie2-build) -- CSV file

Question

[tea.vuki]

Hi all,

There's a -c option in bowtie2 indexer stating "The reference sequences are given on the command line. I.e. <reference_in> is a comma-separated list of sequences rather than a list of FASTA files."

Does this mean that I can provide csv file as an input for bowtie2-build or only literally comma-separated list of seq provided directly to command line?

Answer 1

[GenoMax]

While it is tempting to ask questions this is an example where you could simply try the operation out. It is not going to cause any big problems and you will get your answer in the process.

Yes, you simply provide a comma separated list of file names.

[tea.vuki]

That wasn't my question and arrogance isn't necessary. I tried everything several times on my own, believe me. But when you are not sure whether results you are getting are valid, it's good to double check.

[GenoMax]

You question was

Does this mean that I can provide csv file as an input for bowtie2-build or only literally comma-separated list of seq provided directly to command line?

which I answered above. There is no arrogance implied. We are trying to help everyone.

I tried everything several times on my own, believe me

Are you running into a problem? You have not described the problem, if you are.

[tea.vuki]

My question was does bowtie2 indexer accept CSV files. When I provide CSV file or comma-separated list of seq I get the same result with both. However, they both differ from the one I'm getting with the FASTA file used to generate CSV file.

[GenoMax]

FASTA file used to generate CSV file

What does that mean exactly?

You would either make a CSV format file with the names of the individual fasta in it or simply provide them as a comma separated list on the command line itself.