Understanding Read Groups for single end and paired end data

[imsharmanitin]

Dear All,

I am new to GATK and very confused regarding "Read Groups". I have fastq files and I will like to add read groups to the files. This is what I have understood and please do let me know where I am correct or wrong.

Case1: Single-End data
Let's say I have 2 samples S1, S2 sequenced in 3 lanes.
This will give rise to 3 fastq files, i.e. S1_L1.fastq.gz, S1_L2.fastq.gz, S1_L3.fastq.gz, S2_L1.fastq.gz, S2_L2.fastq.gz and S2_L3.fastq.gz

Now what I have understood from reading numerous blogs and GATK forum that the read group ID should be unique and is used to correction for the variation between reads of the same sample from different lanes. Like we can find if the there is something wrong with a single lane
Hence, it should look like following

RGID=S1_L1 PL=illumina SM=S1
RGID=S1_L2 PL=illumina SM=S1
RGID=S1_L3 PL=illumina SM=S1
RGID=S2_L1 PL=illumina SM=S2
RGID=S1_L2 PL=illumina SM=S2
RGID=S1_L3 PL=illumina SM=S2

Is there some other application of read group id?

Case2: Paired-End data
How will we define read groups if the data was paired-end, such as

S1_L1_R1.fastq.gz, S1_L2_R1.fastq.gz, S1_L3_R1.fastq.gz, S2_L1_R1.fastq.gz, S2_L2_R1.fastq.gz and S2_L3_R1.fastq.gz

S1_L1_R2.fastq.gz, S1_L2_R2.fastq.gz, S1_L3_R2.fastq.gz, S2_L1_R2.fastq.gz, S2_L2_R2.fastq.gz and S2_L3_R2.fastq.gz

[GenoMax]

This is hardly ever the case. Now-a-days technical part of sequencing has become almost perfect. If a lane had some problem (e.g. a bubble during sequencing) your sequencing provider should not release that data in the first place.

Like we can find if the there is something wrong with a single lane