Where should I cut my sequences? (Left y Len: ideal value)

Hi @Wen,

Welcome in the forum!

Could you give bit more context on the data to help us help you please?
Such as: what gene you working on, which region, if you know the expected length of that,
what sequencing platform you used, if these reads were preprocessed and so on. Do not forget the qiime version you are using!

I also would like to hear your idea on your question and the reason behind, did you try any setting ... did you get any error or few resulting reads? I believe it would be much better for your learning to open a discussion rather then throwing figures and waiting for answers!
(There is even now a paragraph on the Code of Conduct trying to explain that we don't like/want do the job for you! ... it makes our life here boring and is not helpful to you either :wink:). If you need a starting point, the tutorial are always there for this reason!

I hope it make sense to you!
Best
Luca

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Hi Luca, thank you very much for your suggestions.
I am working on the 16s gene, specifically the V4 region, the expected length of which is 254 bp. Illumina MiSeq was the platform it was sequenced on. The reads were delivered to me demultiplexed and I imported them to Qiime2 and built the summary table. Taking into account the mean, the Interactive Quality Plot considered that the ideal left value was 0 and the len value 220, I wanted to know if these values ​​were correct, since the expected length is 254, and if this later affects the taxonomic classification?

It was sequenced on a V3 board, 150 pairend.

Hi @Wen,

Thanks for the information. Working with V4, I expect the reads overlapping for most part, so the truncating parameter you suggesting should work.
Do you know if these sequences have been pre-processed to remove PCR-primers? Form the plot I guess not. If this is true, you should remove all the non-biological sequences before the dada2 step!

I am sorry but the second message is confusing to me, the plots you attached are showing 300 bp in both R1 and R2, so the sequences can not be obtained on a 2x150 bp lane. Could you double check please?

Hope it helps
Luca

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You are right, they are 2X300 (600 cycles).