Meaning of -c option backward?

[rsharris]

I didn't use -c on my replong command line.

The output tells me "correction=false" Then later says "Use corrected reads"

Is that the correct behavior? Or should it correct reads when $cor is true, and use raw reads when $cor is false?

[rsharris]

Also not clear whether the example "drosophila test file of 100k reads" contains raw reads or corrected reads. If I use this file for testing, should I use the -c option or not?

[bzvew]

Hi, I'm sorry for that misunderstanding. If you use corrected reads, you do not correct the read by canu again. The default behavior is cor=false. If you set -c true, canu will correct the reads (raw or corrected reads input) by correctReads.sh. So when "correction=false", replong will output "Use corrected reads", because replong assumes the reads are corrected before. If "correction=true", replong will output "Use raw reads", and correctReads.sh will be used in the process.

The reads human_100k.fa are corrected reads and dro_100k.fa are raw reads. However, -c can be set to true anyway to have better read quality.

[rsharris]

I see. I misinterpreted it as indicating I was giving it corrected reads, rather than indicating that the correction step is needed.

It might be clearer to if line 219 reported "correcting raw reads".

Regarding correctReads.sh, I don't see any script by that name in replong. Perhaps it is part of canu? But in any case I don't see it called directly from replong.sh. Regardless of whether cor is true or cor is false, canu -correct is run, albeit with a couple different parameters (for some reason the param order has been shuffled between lines 220 and 227, making it look like there are more differences than there really are).

[bzvew]

Yes, correctReads.sh is in Canu. "canu -correct" means canu will stop after correction. However, it can stop after calculating overlap by "stopAfter=overlap", so for the corrected reads the real correction step will not be used.