Import Single End-Forward Reads

[fabipc (Fabiola)]

Hello,

I have a quick question. I was given dual barcode data for analysis of 16S. I was able to properly import the files as single-emp-sequences as per "moving pictures tutorial", however I have one library that was demultiplexed but the files do not look like normal fast.q files so I am unsure how to import them.

The files read as (P.S. we are only using forward reads as the reverse reads are pretty bad)
mR319-L1-P243-GCTTCCAGTTAA-TGTCTCGCAAGC-READ1-Sequences.txt.gz

I read this topic here, and attempted importing using the tutorial (see below) but given the format of the files I continously get the error below.

qiime tools import
--type EMPSingleEndSequences
--input-path Sequences/ForwardReads
--output-path Plate2/Emp-SingleEnd-SeqRaw-2.qza

*There was a problem importing Sequences/ForwardReads:
*Missing one or more files for EMPSingleEndDirFmt: 'sequences.fastq.gz'

If you could please let me know how to proceed, I would really appreciate it.

Thanks,
Fabi

[cherman2 (Chloe Herman)]

Hi @fabipc,
When you import EMPSingleEndSequences, QIIME 2 is expecting a file called sequences.fastq.gz

It wants a fastq.gz file and you have a txt.gz file. So, we need to figure out if your data is in fastq format and labeled txt or if it needs to be reformated.

The easiest way is to peek into the file and see how it is formated.
Could you run and post a screenshot of the output?

zcat your_filename.gz | head

Thanks