Split paired end multi-sample fastq to single-sample fastq

nofutur · 01-29-2019, 09:21 AM

Hi,

I have a single, multi-sample FASTQ file containing paired end reads from dozens of samples. I would like to split this file into individual sample-level FASTQ files.

Code:

@SRR0000001.1.1 HISCAN01_77:4:1104:20579:289221 length=100
GCTGGA
+SRR0000001.1.1 HISCAN01_77:4:1104:20579:289221 length=100
@@<BDDAD;A<<CC+2AEFFBFH>EG###########
@SRR0000001.1.2 HISCAN01_77:4:1104:20579:289221 length=100
GCTCTA
+SRR0000001.1.2 HISCAN01_77:4:1104:20579:289221 length=100
B?;DDBD;8DD))
@SRR0000002.2.1 HISCAN01_61:2:2204:29774:93471 length=100
GCTTGC
+SRR0000002.2.1 HISCAN01_61:2:2204:29774:93471 length=100
BCCFFFFFFHHHHJJJJJJJJJJJJ:ACDD9AACDD

I would like to split this file into the following files:

Code:

SRR0000001_1.fastq
SRR0000001_2.fastq
SRR0000002_1.fastq
SRR0000002_2.fastq
SRR0000003_1.fastq
SRR0000003_2.fastq

I would appreciate your help.

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