How to analyse different sample number fastq files

Question

[majeedmj.ict]

Hello, I got paired end sequences with different sample number and lane number (showing one sample fastq files below) .

1) D3M0_S1_L001_R1_001.fastq.gz 2) D3M0_S45_L002_R1_001.fastq.gz

3) D3M0_S1_L001_R2_001.fastq.gz 4) D3M0_S45_L002_R2_001.fastq.gz

Should i Merge S1 and S45 using cat ? or should i perform seperately each S1 and S45 and get individual read count data ?

what is the better approach for downstream analysis of RNAseq analysis?

if i need to merge , what is the better approach ?

[benformatics]

Are they the same sample? If they are both actually the same sample then I would merge, otherwise treat them as replicates.

Answer 1

[GenoMax]

It is odd that you have two different S* numbers of the same sample in different lanes. Generally one should have the same S* for the same sample in different lanes.

But to answer your question, if it is the same sample then you can cat the two files together.

[Istvan Albert]

perhaps the sample sheet provided to the converter listed these as separate samples.