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Merge two .fastq files from two different lane

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

loop ngs merge fastq cat
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updated by GenoMax GenoMax • written by k.kathirvel93 k.kathirvel93

yes, and the issue/problem being ?

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written by lieven.sterck lieven.sterck

2 answers

from two different lane using cat command with bash for loop

Answers here: Concatenating fastq.gz files across lanes

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written by GenoMax GenoMax

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
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written by Istvan Albert Istvan Albert

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