Illumina read naming

[BaCh]

Hi,

I recently got a file with Illumina data where the reads are named like this:

HWI-ST525_0039_8_1_3566_2216#GACCAC/1
HWI-ST525_0039_8_1_3673_2244#ACTTGG/1
HWI-ST525_0039_8_1_3520_2247#CCTGAC/1
HWI-ST525_0039_8_1_3803_2237#ACCCCC/1
...

Can anyone tell me what the 6-nucleotide part between the hash and the slash stand for? (e.g. #ACTTGG). The rest is clear, but that part is a new naming scheme for me.

While I suspect that I'm not the first to ask this, it looks like my Google-Fu is failing me when searching for the answer.

B.

[kmcarr]

This represents the index read. Apparently a pool of samples was run in this lane, with each sample having a specific barcode sequnce attached during its respective library prep. The reads can be sorted based on these index sequences. You would need to discuss with your sequncing center which sample is associated with which index sequnce.

[BaCh]

This represents the index read. Apparently a pool of samples was run in this lane, with each sample having a specific barcode sequnce attached during its respective library prep. The reads can be sorted based on these index sequences. You would need to discuss with your sequncing center which sample is associated with which index sequnce.

Funny thing is: it was just one sample. Paired-end, but definitively just one sample in one lane. I suspect they took the wrong pre-processing pipeline then.

Thank you very much,
Bastien

[kmcarr]

Funny thing is: it was just one sample. Paired-end, but definitively just one sample in one lane. I suspect they took the wrong pre-processing pipeline then.

Thank you very much,
Bastien

Hmm...that is suspect, and taking a closer look at the actual index sequences in your example, none of them match the Illumina tag set. I guess it's time to have a chat with your sequencing provider.

[NextGenSeq]

A lot of people don't use the Illumina tags since other vendors kits are cheaper (and mostly better).