Dada2 determining truncate problem

Hi, I have a fastq file that contains forward reads from iontorrent. My friend told me that those are belong to v3-v4 region of the 16S rRNA gene. By using qiime 2 I completed all processes until dada2. However when I visualize the data to determine parameters to truncate and trim I see that the plot (x axis:Sequence base, y axis: Quality Scores) reaches 2000 base on x axis. Does the x-axis show sequence length? Namelly is it means I have sequences have length 2000 base? I'm sorry if the question sounds nonsense I guess I misunderatood something while reading the plot. Thanks

Hi @kubra,
The x-axis does tell you the length of the sequences. So it seems like you got long reads

Additionally at the bottom of the page with the graph you just referenced has this table:

This tells you the distributions of sequence length. This is a screenshot of the table from the moving pictures tutorial. Here you can see that all the sequences in this data set are 152 nts.

If you want to post screenshots, I can help you confirm!

Hope this helps! :turtle:

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Thank you for confirming. Since the data is not mine I'm not able to share but I would love to. Since he told me that data belongs to v3-v4 and I saw sequences reach 2000base I doubt myself:) Because 16S rRNA itself reaches ~1500bp. Maybe he is wrong with the data region/gene right? Thanks a lot again🙏

hi @kubra

Totally understand! No worries

I am not quite sure! I think your best way forward is to bring this viz to your friend who knows about what region/ how it was sequenced and discuss with him!

Hope that helps!

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@cherman2 We will see:) Thanks for your time✨️

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