I am running 26 paired end sequences (16s RNA) which is sequenced through illumina platform PE 250.
I demuliplexed the data and the demultiplexed files is attached below:
demux-paired-end.qzv (288.4 KB)
I have following questions:
I trimmed both forward and reverse sequences and the trimmed file is as follow:
trimmed-remove-primers.qzv (293.9 KB)
- When I am opening both qzv files, I observed for the forward reads, the quality drops a lot for the sequences which are greater than 220 bases. For the reverse reads, the bases are cut after 225 bases and the quality is still low.
As far as I understood, after trimming step, quality should increase but its decreasing. Can someone please help me to understand.
- Based on the trimmed-remove-primers.qzv file, I am using the following code for dada2 processing but its running for hours. I am not sure if its okey. I am using virtual machine and I have alloted 20000 MB memory space to VM.
Thank you in advance!