Question about -d parameter?

[HJTsai]

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?

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]

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]

Hi,

Thank you for your reply.

HJTsai

[HJTsai]

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

[rvolden]

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

[HJTsai]

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]

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.