Thanks for taking time to answer my query. I am fairly new to qiime2 and using dada2 plugin in qiime2 for denoising my paired-end reads data. My target amplicon size is ~ 458 bp whereas I am getting features of varying lengths from 240 to 458.
I am using following command line:
qiime dada2 denoise-paired --i-demultiplexed-seqs paired-end-demux-V2.qza --o-table table-V2 --o-representative-sequences rep-seqs-V2-24030 --p-trunc-len-f 240 --p-trunc-len-r 240 --output-dir Denoised-V3
How can I avoid the shorter reads?
Thanks a lot
Thanks a lot @Nicholas_Bokulich
Just for my knowledge, why are we getting shorter read lengths despite the fact that we are truncating both the forward and reverse reads. Theoretically it should discard anything shorter than that (in my case forwrad<240 and reverse<230). So I should not get such short reads like 300, 320 or so. Please give your insights. Thanks
Because truncation happens before denoising and joining. So you are truncating to 240 nt, but then joining (merging) your reads and some are overlapping a lot, yielding a short read.
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