Hi, I have a simple question using denoise-ccs.
I am trying to analyze long read sequencing data using dada2 denoise-ccs, but when I try to truncate it by specifying the length using --p-trunc-len, it is shorter than the desired length, so I am trying to truncate it using --p-trunc-q. I have a question.
If I specify --p-trunc-q 10, I want to truncate the bottom 25% of q scores lower than 10. Can you tell me where this q10 is based on?
Hello @eysung,
but when I try to truncate it by specifying the length using --p-trunc-len, it is shorter than the desired length
That's not supposed to happen, could you upload the resulting representative sequences artifact in which you're observing lengths that differ from your parameter?
If I specify --p-trunc-q 10, I want to truncate the bottom 25% of q scores lower than 10. Can you tell me where this q10 is based on?
Providing --p-trunc-q 10 will truncate all reads at the first position that a quality score of less than 10 is detected. There is no inherent percentile interpretation.
Hi @colinvwood ! Thank you for your reply!
Here is the command I used:
qiime dada2 denoise-ccs --i-demultiplexed-seqs 1_import/ON/import_pre_ON.qza --p-front AGRGTTYGATYMTGGCTCAG --p-adapter TACGGYTACCTTGTTACGACTT --p-trim-left 12 --p-trunc-len 1570 --o-table 3_denoising/pre_ON_table.qza --o-representative-sequences 3_denoising/pre_ON_repseqs.qza --o-denoising-stats 3_denoising/pre_ON_stats.qza
And here is the error message:
Plugin error from dada2:
No reads passed the filter. trunc_len (1570) may be longer than read lengths, or other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
And I attatched summary file I checked too.
ON_init.qzv (368.0 KB)
This data was generated with MiniON, but there is no MiniON-specific plugin in qiime2, so I did it this way.
I really need to analyze the MiniON data, and I only have about 2 weeks left to do so. If denoise-ccs can't analyze MiniON data, can you tell me if there is a way to analyze MiniON data among the current plugins in qiime2, and if not, when you plan to support it?
Thanks in advance!
EY
Hello @eysung,
No reads passed the filter. trunc_len (1570) may be longer than read lengths, or other arguments (such as max_ee or trunc_q) may be preventing reads from passing the filter.
This is important. Did you inspect your reads using the demux summarize visualization to confirm that 1570 isn't longer than your reads?
This is probably moot however because the denoise-ccs action is not suitable for minion data. In fact, no dada2 action is suitable for minion data according to dada2's developer, see here.
Thank you for your reply, @colinvwood !
That's a sad story.. Then is there any recommend way to analyze MiniON data?
As I said before, I have only 2 weeks to finish analyze with qiime2.
Anything would be appreciated!
EY
Hello @eysung,
No, to my knowledge there are no actions intended to process Oxford Nanopore sequences.