Merge two .fastq files from two different lane

Question

[k.kathirvel93]

Hi Every One,

How to Merge two .fastq files from two different lane using cat command with bash for loop. My file name looks like this

> RFNB-2939_S193_L001_R1_001.fastq,  RFNB-2939_S193_L002_R1_001.fastq, 
> RFNB-2951_S194_L001_R1_001.fastq,  RFNB-2951_S194_L002_R1_001.fastq.

Thanks in advance

[lieven.sterck]

yes, and the issue/problem being ?

Answer 1

[GenoMax]

from two different lane using cat command with bash for loop

Answers here: Concatenating fastq.gz files across lanes

Answer 2

[Istvan Albert]

that is what cat does, concatenates

Concatenate a,b into c

cat a b > c

in your case:

cat RFNB-2939_S193_L001_R1_001.fastq RFNB-2939_S193_L002_R1_001.fastq > RFNB-2939_S193.fq 

cat RFNB-2951_S194_L001_R1_001.fastq RFNB-2951_S194_L002_R1_001.fastq > RFNB-2951_S194.fq