Is it possible to change step size?

[mtnouchi]

Hello

I would like to count equally spaced k-mers. e.g.) in-frame k-mers (such as codons or bi-codons) with step size 3.

Is it possible with Jellyfish?

Thank you

[gmarcais]

This is not supported by default. Can I ask how you would see something like this work? You would pass a step size and, maybe, an offset. For each sequence in a fasta or fastq file, first step forward by the offset, then return the k-mer every step size. Is that what you envision?

[mtnouchi]

Sorry for the late reply.

Yes, that's exactly what I meant. Passing an offset as well as a step size would be great!!

[gmarcais]

It seems interesting. I'll try to implement it.

How would an N be handled? Like it is the start of a new sequence?

[mtnouchi]

Thanks a lot! I'm looking forward to it.

In my case, I don't want k-mers that contain N to be treated as such. Some assembled coding sequences still contain N, Y, R etc. So, I would like N to be just ignored so as not to disrupt the reading frame.

However, in some other cases, like the arbitrary nuber of Ns representing gaps, it would be better to handle them as the start of a new sequence.

Therefore, I would be grateful if the behavior of the program could be specified through a switch.