Converting lowercase sequences to uppercase in Fastq file

[Rasit_Asiloglu]

Hello!

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
--type 'SampleData[SequencesWithQuality]'
--input-path manifest.tsv
--output-path demux.qza
--input-format SingleEndFastqManifestPhred33V2

However, it give error " Lowercase case sequence on line 6"

Does anyone help me with converting the lowercase sequences to uppercase?

[colinbrislawn (Colin J Brislawn)]

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:

@Rasit_Asiloglu

However, it give error " Lowercase case sequence on line 6"

That's pretty unusual! How did that happen? Was there some preprocessing or masking applied to your fastq files before importing into Qiime2?

[Rasit_Asiloglu]

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.