How can we trim or truncate for these kind of quality plots? Although I am getting good number of reads per sample but having huge ranges (10k to 200k).
Hi @dasqiime22,
The range of your sample’s depth shouldn’t really affect your trim/truncating decision making process.
As for how to trim/truncate, this really depends on what tools you are using.
If you are using DADA2, it has its own set of parameters such as --p-trunc-len-f/r and --p-trim-left-f/r you can see more details in its help file.
Deblur uses --p-trim-length and --p-left-trim-len (see here for details).
As for how to select these, there are a lot of considerations to account for and you can search through the forum for various discussions and recommendations on how to select these parameters.
Good luck!
I saw this question in qiime2 forum.
Why I am asking this questions is that I see vary good quality reads almost>=30 for my case. In that do I need any trim/truncate?
Thanks
Hi @dasqiime22,
Your original question was asking about HOW to trim/truncate, which is why I pointed towards the commands for those tasks.
Your next question here is asking whether you need to truncate or not. As you pointed out you have high quality reads so just try not truncating anything and you can always compare the results to another run where you truncate some. It’s always better/more fun to learn by doing than taking other people’s word on it, especially with regards to situations like this where there is no right answer.
2 Likes
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.