Question: chop Nanopore (long) reads
0
gravatar for lijingtang2010
6 months ago by
lijingtang20100 wrote:

Do you know if there are tools to chop reads from Nanopore sequencing at given positions?

sequencing nanopore alignment • 326 views
ADD COMMENTlink modified 6 months ago by ATpoint30k • written 6 months ago by lijingtang20100

If your question fits in one sentence then you probably didn't explain it sufficiently, please elaborate.

ADD REPLYlink written 6 months ago by WouterDeCoster43k
1

The question is fine, my response will be: "Yes"

ADD REPLYlink written 6 months ago by JC9.5k

Do you have any suggestion?

ADD REPLYlink written 6 months ago by lijingtang20100

Sorry for that, I want to chop Nanopore reads at given positions and each read was chopped at different positions.

ADD REPLYlink written 6 months ago by lijingtang20100

I want to chop Nanopore reads at given positions and each read was chopped at different positions

It is not clear what you mean by this. You want to chop individual reads at certain positions (different for each read?) OR are the reads chopped at different length and you want to make them all the same length by chppoing?

ADD REPLYlink modified 6 months ago • written 6 months ago by genomax78k

Thank you for your reply. I want to chop individual read at certain positions (coordinates from alignments). For instance, read A 3-500, 800-901; read B 2-50; read C......

ADD REPLYlink written 6 months ago by lijingtang20100

Before this goes back and forth now, please give a reprodubibly and illustrative example. Post an example input and a representative example output. It is still clear what exactly you aim to do.

ADD REPLYlink written 6 months ago by ATpoint30k

Now, I try to convert fq to fa, then use bedtools to mask.

ADD REPLYlink written 6 months ago by lijingtang20100
2

a representative example

I do not want to appear rude but you have now four experienced people in this thread involved who all could provide you with an answer or even a working script but you lack to provide a suitable example of how the input data look, how exactly you want to trim and what the expected output is. I for my part will therefore withdraw from this thread. For the future you should avoid annoying people with this attitude. A simple example of what you have, what you want (show data, not just words) and what you've tried will motivate people to give you good answers. Brief Reminder On How To Ask A Good Question

ADD REPLYlink written 6 months ago by ATpoint30k

If you have specific intervals you want to chop from individual reads then you would likely need to write some custom code to do that.

ADD REPLYlink written 6 months ago by genomax78k
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