WES data PAir-end Sequencing ??

Question

[deepue]

Hi,

I have got the below files from the sequencing laboratory

Sample_L001_R1_001.fastq
Sample_L001_R1_002.fastq
Sample_L001_R1_003.fastq
Sample_L001_R1_004.fastq
Sample_L001_R1_005.fastq
Sample_L001_R1_006.fastq
Sample_L001_R1_007.fastq
Sample_L001_R2_001.fastq
Sample_L001_R2_002.fastq
Sample_L001_R2_003.fastq
Sample_L001_R2_004.fastq
Sample_L001_R2_005.fastq
Sample_L001_R2_006.fastq
Sample_L001_R2_007.fastq
Sample_L002_R1_001.fastq
Sample_L002_R1_002.fastq
Sample_L002_R1_003.fastq
Sample_L002_R1_004.fastq
Sample_L002_R1_005.fastq
Sample_L002_R1_006.fastq
Sample_L002_R1_007.fastq
Sample_L002_R2_001.fastq
Sample_L002_R2_002.fastq
Sample_L002_R2_003.fastq
Sample_L002_R2_004.fastq
Sample_L002_R2_005.fastq
Sample_L002_R2_006.fastq
Sample_L002_R2_007.fastq

I could understand that

L** represents lane, what else information about the sequencing can be drawn from these naming conventions. Could someone throw light?

Many Thanks

Answer 1

[Devon Ryan]

Sample is the sample name, L??? is the lane, and R? is the read number (1 or 2), which is only meaningful for paired-end sequencing. The last 3 digits don't have any real meaning; the reads are just put into multiple smaller files instead of a single larger one. Note that, for example, Sample1_L001_R1_001.fastq and Sample1_L001_R2_001.fastq describe the same read pairs, so make sure to always process them together. The number of files per sample is then just determined by the sequencing depth and how large those files are set to be.

[deepue]

Thanks Devon.