Extracting species abundance from uBiome FASTQ outputs about fratjuice

[dhimmel]

For a single sequencing run (ssr_300909.zip in this example), there are multiple FASTQ files:

ssr_300909__R1__L001.fastq.gz
ssr_300909__R1__L002.fastq.gz
ssr_300909__R1__L003.fastq.gz
ssr_300909__R2__L001.fastq.gz
ssr_300909__R2__L003.fastq.gz
ssr_300909__R2__L004.fastq.gz

In ssr_300921.zip there are:

ssr_300921__R1__L002.fastq.gz
ssr_300921__R1__L003.fastq.gz
ssr_300921__R1__L004.fastq.gz
ssr_300921__R2__L001.fastq.gz
ssr_300921__R2__L002.fastq.gz
ssr_300921__R2__L003.fastq.gz
ssr_300921__R2__L004.fastq.gz

So what do the multiple parts of these file names refer to?

My understanding is that R1/R2 refers to the paired end sequencing, such that R1__L002 and R2__L002 contain the respective ends of the same sequences? However, there's not always a compliment (not every R1 has an R2), which confuses me.

The L001 through L004 refer to sequencing lane? Multiple samples are sequenced in the same lane, but the demultiplexing has already been performed, so only sequence for the listed sample are part of the FASTQ file?

[dhimmel]

Additional References

• Qiime2 Forum: Analysis of UBiome Data - Roadblocks & Questions