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rvolden / C3POa

Computational pipeline for calling consensi on R2C2 nanopore data
GNU General Public License v2.0
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Question about -d parameter? #9

Open HJTsai opened 5 years ago

HJTsai commented 5 years ago

Hi,

-d median distance between peaks cutoff. This should be the length of your shortest input sequence in your library preparation. Defaults to 500

I have a question about -d parameter. What's the mean of median distance between peaks cutoff?

splint

Median distance = median length of a1 and b1 or median length of a1, b1 and a2 or other? Between peaks means between two splint sequence?

Thanks.

HJTsai

rvolden commented 5 years ago

Median distance is calculated on a per read basis, so it would be the median of a1 and b1. You would usually set this as the smallest length of your input cDNA before circularization.

HJTsai commented 5 years ago

Hi,

Thank you for your reply.

HJTsai

HJTsai commented 5 years ago

Hi, Dose it means read without splint sequence or only one splint sequence will be removed ? Thanks. HJTsai

rvolden commented 5 years ago

Reads without splint sequences are removed during preprocessing. Reads with one splint sequence are usually okay.

HJTsai commented 5 years ago

If reads with one splint sequence, how to calculate the -d median distance between peaks cutoff? If reads with partial splint sequence, reads will be removed during preprocessing or ?

rvolden commented 5 years ago

If there's one splint sequence, it won't calculate the median distance, but it will try to make it into a zero repeat read. If there's a partial splint sequence, it will probably get removed during preprocessing.