What does S1 , L004 , R2 , 001 stand for in HCC###BL_S1_L004_R2_001.fastq?

Question

[bshifaw]

What does S1 , L004 , R2 , 001 stand for? for example HCC###BL_S1_L004_R2_001.fastq

Answer 1

[GenoMax]

HCC###BL - Sample Name that was provided in samplesheet
S1 - Row in the Sample Sheet
L004 - Lane the sample ran in
R2 - Read 2 from a paired-end dataset
001-00N - Would be numbers in sequence, if the file is provided in chunks instead of one (then it would just be 001).

Answer 2

[Ram]

Please google before you ask.

http://support.illumina.com/help/SequencingAnalysisWorkflow/Content/Vault/Informatics/Sequencing_Analysis/CASAVA/swSEQ_mCA_FASTQFiles.htm

EDIT: The above link is for an older format, apparently. Please ignore it.

FOLLOW-UP EDIT: Looks like this format is still in use. It's getting hard to tell when I'm right and when I'm wrong :)

[GenoMax]

@Ram: You linked the example for CASAVA, which is so subtly different then bcl2fastq2 (which is the current version). I explained it above.

[GenoMax]

Your link is still valid for CASAVA or bcl2fastq v.1 style output which was not directly applicable in the example @bshifaw had included. Some people who don't have NextSeq/HiSeq3000/4000 still continue to use bcl2fastq v.1.