question about --p-trim-left --p-trunc-len

[Javad32 (Javad)]

Hello All
I was using these commands for my analysis and I got this graph. What number should I use for --p-trim-left --p-trunc-len ? (qiime tutorial is suggesting 120bp for their example but for my sequence, it looks like a line).

I used V5-V6 as my target and it is around 280bp and with barcode and adaptors 350bp. And the sequencer is Ion Torrent S5.

qiime cutadapt demux-single --i-seqs multiplexed-seqs.qza --m-barcodes-file metadata.tsv --m-barcodes-column Barcode --p-error-rate 0 --o-per-sample-sequences demultiplexed-seqs.qza --o-untrimmed-sequences untrimmed.qza --verbose

4- qiime cutadapt trim-single --i-demultiplexed-sequences demultiplexed-seqs.qza --p-front ATTAGATACCCYGGTAG --p-error-rate 0 --o-trimmed-sequences trimmed-seqs.qza --verbose

5- qiime demux summarize --i-data trimmed-seqs.qza --o-visualization trimmed-seqs.qzv

6- qiime dada2 denoise-pyro --i-demultiplexed-seqs demux.qza --p-trim-left 0 --p-trunc-len 120 --o-representative-sequences rep-seqs-dada2.qza --o-table table-dada2.qza --o-denoising-stats stats-dada2.qza

[thermokarst]

We can not provide private support - I am moving this post to the public forum - please wait for a reply there. Thanks.

[Javad32 (Javad)]

One more question: How can we get more numbers (more sequence base) on X-axis? so we will be able to see where the quality score is dropping down.

[thermokarst]

@Javad32

What number should I use for --p-trim-left --p-trunc-len

Personally I would try to proceed without trimming and then see how the dada2 step goes.

@Javad32

How can we get more numbers (more sequence base) on X-axis?

Zoom in. You can do this by clicking and dragging a rectangle on the plot. To reset, double-click.