I had two samples, each sample are illumina pair-end sequenced. I imported them and joined the pair-end sequence with
qiime vsearch join-pairs --i-demultiplexed-seqs demux.qza --o-joined-sequences demux-joined.qza
then put the .qza to .qzv
demux-joined.qzv (286.5 KB)
then, I did the quality filtering,
qiime quality-filter q-score-joined --i-demux demux-joined.qza --o-filtered-sequences demux-joined-filtered.qza --o-filter-stats demux-joined-filtered-stats.qza
then, I did the deblur step. According to the demux-joined.qzv, I trimmed them at length of 400. I tried three set of parameters, each is:
--p-min-reads 10 --p-min-size 2 (default parameter)
--p-min-reads 0 --p-min-size 0 (I did this because I do not want to delete any low-count sequence)
--p-min-reads 1 --p-min-size 2 (Thanks to @wasade , change to --p-min-size to 2 may be better than 0)
The outcome are:
deblur-stats400-default.qzv (191.7 KB)
deblur-stats400-00.qzv (191.7 KB)
deblur-stats400-12.qzv (191.7 KB)
The thing goes weird as shown in deblur-stats400-00.qzv. In the sample SRR1460604, none of the sequences passed the positive filter, which seems impossible. In deblur-stats400-default.qzv, even if low-count sequence is deleted, there is still some sequence passed the positive filter. Why?
In the third .qzv file, it seems everything went smoothly....I think if I want to retain the low-count sequence, set the parameter to --p-min-reads 1 --p-min-size 2 will be better. But solve this problem may make me settled...