Question about final command

[Tdanis]

Question about final command

[holtjma]

I'm not entirely sure I understand your question, but the main output of fmlrc (i.e. corrected reads) will be whatever filename you specify for <corrected_reads.fa>.

[Tdanis]

So here we specify the output file and before this the input file? Am I wrong? Theodoros Danis

…

________________________________ From: Matt Holt <[email protected]> Sent: Saturday, November 16, 2019 9:38:59 PM To: holtjma/fmlrc <[email protected]> Cc: Tdanis <[email protected]>; Author <[email protected]> Subject: Re: [holtjma/fmlrc] Question about final command (#12) I'm not entirely sure I understand your question, but the main output of fmlrc (i.e. corrected reads) will be whatever filename you specify for <corrected_reads.fa>. — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#12?email_source=notifications&email_token=AKQNXT7OKYHIN2LDLXZUS5DQUBD5HA5CNFSM4JOGP7N2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEHY5NA#issuecomment-554667700>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKQNXT6H2J5CRTIK7GZGQ4TQUBD5HANCNFSM4JOGP7NQ>.

[holtjma]

That's incorrect. The things with brackets (<...>) are placeholders for your filenames.

If your BWT is at /path/to/my/bwt/comp_msbwt.npy AND
Your original reads are at /path/to/my/sample/raw_reads.fa AND
You want to store your output at /path/to/my/sample/corrected_reads.fa THEN
The full command would look like this:

./fmlrc /path/to/my/bwt/comp_msbwt.npy /path/to/my/sample/raw_reads.fa /path/to/my/sample/corrected_reads.fa

[Tdanis]

Thank you very much.