How do I know if my files are demultiplexed?

Question

[Bruna]

Hello!

I'm writing because I'm new at this and I'm having some difficulty understanding if my files are already demultiplexed or not.

I have 80 fastq files (40 forward + 40 reverse), and inside there are several entries however where the index or barcode should be there is the same number (same for the r1 and respectively r2 file) and they look like the following:

Could someone give me a hand?

Answer 1

[GenoMax]

In the sample of fastq data you posted (please copy and paste text next time instead of using images for this) there are no indexes in the fastq headers. If your fastq data was indexed (and unless the files were not manipulated in some way) the header should include the sequence of the indexes. (ref: https://en.wikipedia.org/wiki/FASTQ_format#Illumina_sequence_identifiers )

It is possible that you have data that is not multiplexed or at least the index information may be missing. It is also possible that the index reads are present in separate files.

Do all your files look like this? Are there any files with short fastq reads (that may be index sequences).

[Bruna]

yes next time will do that

all of my files look like this, and I was not given more files than this ones in the link you send they say this about my type of samples:

"Note that more recent versions of Illumina software output a sample number (defined by the order of the samples in the sample sheet) in place of an index sequence when an index sequence is not explicitly specified for a sample in the sample sheet. " so maybe the data is already demultiplexed

(thank you very much for your help!)

[GenoMax]

so maybe the data is already demultiplexed

Indeed it must be. You will need to get the samplesheet in order to figure out which row number in it correspond to which sample.