So I recently got involved in a collaboration with some people on my campus. Essentially the researcher had contracted with Ubiome to do their sequencing, but then the company went bankrupt and didn’t fulfill their end of things. They ended up with a bunch of raw data, and I was asked to join in. I am excited, but a little unsure of the importing of the data.
I have 35 samples, but the number of files per sample is confusing me. I have eight fastq/GZ files per sample, 4 of them are R1 and 4 of them are R2. The number of files doesn’t seem to match up with anything I’ve found on Qiime docs.
Now, I am used to having one forward and one reverse file, and am confused by this number of samples. I didn’t do the sequencing myself, but I was told they used the following from Almonacid et al., 2017.
“Consolidated libraries were quantified by quan- titative real-time PCR using the Kapa Bio-Rad iCycler qPCR kit on a BioRad MyiQ before loading into the sequencer. Sequencing was performed in a pair-end modality on the Illumina NextSeq 500 platform rendering 2 x 150 bp pair-end sequences.”
Any help at all would be greatly appreciated! Thanks in advance!
Almonacid, D. E., Kraal, L., Ossandon, F. J., Budovskaya, Y. V., Cardenas, J. P., Bik, E. M., … Apte, Z. S. (2017). 16S rRNA gene sequencing and healthy reference ranges for 28 clinically relevant microbial taxa from the human gut microbiome. PLoS ONE, 12(5), 1–15. https://doi.org/10.1371/journal.pone.0176555