What is the difference between different SRA reads from different lanes for one sample?

Question

[m.koohi.m]

I've searched the CCIS27304052ST-3-0 into SRA ncbi search box and the result are 4 different SRA for this sample. I wonder what is the difference between these SRA data?

http://www.ncbi.nlm.nih.gov/sra/?term=CCIS27304052ST-3-0

I know two of them for single-end and two of them for paired-end in different lanes and for one sample but why two for each one?

Answer 1

[Evgeniia Golovina]

Four sra files from the same one experiment. Differences:

The first two (ERX446419 and ERX446420) are single reads and relate to the 5th and 6th lane.

The last two (ERX444923 and ERX444924) are paired reads and relate the 5th and 6th lane.

Look at the names:

single-end:

CCIS27304052ST-3-0_11s002713-1-1_lane5
CCIS27304052ST-3-0_11s002713-1-1_lane6

paired-end:

CCIS27304052ST-3-0_11s002713-1-1_lane5
CCIS27304052ST-3-0_11s002713-1-1_lane6

[m.koohi.m]

Thank you Evgeniia,

Yes, That is correct! I am new in NGS, What is the differences between lane5 and lane6 and also single-end and pair-end? Could you possibly help me?

[Evgeniia Golovina]

Sure! :)

1) I think, lane 5 and line 6 are possible technical or biological replicates. Need to read about this experiment in more detail.

2) About single and paired reads you can find here.

If you'll still have question, I can help you.

[m.koohi.m]

Thank you,

Also I found these links:

• What Is A "Lane" In Next Generation Sequencing Context?
• http://www.illumina.com/technology/next-generation-sequencing/paired-end-sequencing_assay.html

To be honest, I wanted to apply an algorithm on SRA data of this sample but I am a bit confused that which one should be chosen to download!! There is not any clues in the papers about the different lanes and pared and single-end modes! I wonder can I just download one of paired-end and work with it as a represent of others or not?

[Evgeniia Golovina]

Yep, it makes sense.

If you want just to try your algorithm on SRA data, you can take any of this 4 samples.

If you are interested to test how your algorithm works on single and paired reads, you can take 2 samples (single and paired)

What algorithm do you want to apply?

Answer 2

[m.koohi.m]

Hopefully I can find the following link:

A Simple Question On Rna-Seq Terminology

We have two different approaches in WGS, the first one is using one lane for different samples. In this way you can save a lot of money and also time, for more details please refer to:

http://www.illumina.com/documents/products/datasheets/datasheet_sequencing_multiplex.pdf

Also another approach is "technical replicates" in this approach you use different lanes for just one sample as technical replicates, to find more about this approach you can read the following article:

http://bioinformatics.bc.edu/marthlab/scotty/help.html