Hello! I have downloaded a single fastq.gz file which contains both Fw and Rv and different samples reads of PE-runs. Is there a way to import these in qiime (without having R1 and R2 indifferent files?) or should I run any other software previously?
How are the reads differentiated? Do the FASTQ headers include information on which direction the read was sequenced in? Can you share the first 10-20 lines of the file? Thanks!
Thanks @botellaflotante! It looks like you have what is known as "interleaved" files. Unfortunately, we don't have support for this directly in QIIME 2 (it has become a bit more uncommon these days, at least from what I have seen here on this forum).
Your QIIME 2 environment already comes with cutadapt, so you could give it a try there, then, once demultiplexed and split up, you could follow a traditional QIIME 2 import.
But I just want to share what I’ve done in the past to quickly split apart interleaved fastq files, in case this serves as a useful backup, or perhaps some inspiration to learn how to use grep!
the first grep grabs headers indicating forward/reverse, and the following 3 lines
the second grep eliminates spacer lines (which grep inserts when the -A option is used)
Thank you! I think qiime cutadapt does not allow the interleaved option, but the grep did the job! Also I had it interleaved because these were many reads downloaded from SRA and this download generated a single interleaved file. I am assuming that there is no need to cut any adapter from these…
I actually found an error with this. The first grep I think it should be '@.*\.1 ' (with a space) Otherwise the output is weird and doesn’t work. Also ‘.1’ alone will result in sequences like ‘.1.2’ or ‘.10.2’ being included in forward…
Thanks again