Importing Merged_Reads.fq into Qiime2 pipeline

[rr220 (R)]

Hello,

I need help with a import command for merged_reads.fq
The sequencing center has not provided individual fastq files for analysis. They sent data as merged_reads.fq format. How do I import this into qiime?

Usually I create raw reads folder that contains FASTQ files for each sample and then use this command:
qiime tools import
--type 'SampleData[PairedEndSequencesWithQuality]'
--input-path
--input-format CasavaOneEightSingleLanePerSampleDirFmt
--output-path demux-paired-end.qza

How should I edit the above command for merged_reads.fq?

I would appreciate your help.

Thank you,
Best,
R

[lizgehret]

Hi @rr220,

Good question! Here's a really helpful answer from @cherman2 regarding importing pre-merged sequences, along with some resources for performing quality control on your data:

Importing alreday merged reads

Hello @NH_20, Welcome to the QIIME2 Community! Here is a tutorial to import pre-merged data. I hope this helps you import your data. Here and here are discussions for how to do quality control with pre-merged reads. If you are unsure how to run quality control commands discussed in those links, I would recommend this section of the moving pictures tutorial. I hope this helps! Chloe

Hope this helps! Cheers