NextSeq 550 Fastq header

[jomare1188]

Hi, im working with PE Nextseq 550 data

I know that there are 12 inline barcodes from 5 to 8 bp for my data

the reads fastq headers shows 57 different dual index sequences (all 8 bp each one) with CGGGGGGG+TGCTTCCA the most prevalent being in the 98% of the total reads

something like this:
@NB501358:172:HTJY7BGX2:1:11101:17581:139461:N:0:CGGGGGGG+TGCTTCCA

does someone know what the 57 sequences means?

thanks

[GenoMax]

Are you sure about inline barcodes?

The example you posted above is standard Illumina index sequences for a dual indexed run. It is common to see a mishmash of combinatorial index sequences (besides those known to be there) in sequence data. They represent errors among other things. I am not sure why you received 57 combinations (it is as if they gave you the remaining data after they took what they wanted). Was this sample run with others that did not belong to you?

[jomare1188]

Thanks for your answer!

Yes i'm sure about the inline barcodes

Yes this data was provided by a external lab most probably was run with other data

[GenoMax]

If "CGGGGGGG+TGCTTCCA" is 98% of the data then you should remove and ignore the rest. You have no idea what is in there if your sample was part of a larger pool. If you are able to recognize the inline barcodes conclusively then you could go fishing in the remainder of the data.