I have demultiplexed and forward and reverse combined sequences per each sample as Fastq file format.
I try to import in Qiime2 with
qiime tools import
However, it give error " Lowercase case sequence on line 6"
Does anyone help me with converting the lowercase sequences to uppercase?
Here's how I would do that with SeqKit
conda install seqkit
seqkit seq input.fastq.gz --upper-case -w 0 > output.fastq
We should also check in about this:
That's pretty unusual! How did that happen? Was there some preprocessing or masking applied to your fastq files before importing into Qiime2?
Thank you very much! It worked!
I obtained the data from a biotech company! Idk the reason but probably they messed up.
They didn't provide any information and they were keep telling me that they can do the bioinformatics for a price! Anyway, I imported the data on Qiime2 and obtained the all data I needed.