Nextseq550, where is the undetermined index files for R1 and R2? (for demultiplexing)

Question

[chloe]

Hi

I'm planning to do troubleshooting my sequencing experiment.

So I tried to open the raw fastq filed released from Nextseq550, and Illumina sequencing machine we got.

What I want to do is demultiplexing undetermined_R1.fastq files by undetermined_index_R1.fastq files.

However, there are only undetermined_R1.fastq files without index info.

Do you know where can I find my index files are?

Answer 1

[GenoMax]

Do you know where can I find my index files are?

There are no separate index files unless they were specifically generated (that does not happen by default). The index information is in the fastq read header even in the "Undetermined" reads file. You can use my answer here C: Demultiplexing reads with index present in the labels to identify indexes present in your data. Once you have that information you can demultiplex the data using a program from BBMap suite (C: Demultiplex Illumina run using custom index configuration ).

[chloe]

Thank you so much for your kind answer!! I'll look into that in a bit more detail tomorrow.