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Paired end SRA generating mutiple fastq files

I tried to convert SRR1652430.sra to fastq:

fastq-dump --split-files SRR1652430.sra

I expected it to produce 2 file for each pair end. However it produces 4 file.

Did I do something wrong or it is ok to get multiple files after conversion.

fasta fastq-dump 454 next-gen-sequencing
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updated by Ram Ram • written by rimjhim.roy.ch rimjhim.roy.ch

Maybe, it's because SRR1652430 reads are both forward? And fastq-dump gives you 2 forward and produces additional 2 reverse files.

Maybe, if you try ./fastq-dump --split-spot SRR1652430.sra, you'll get 2 files.

From fastq-dump manual:

--split-spot - Split spots into individual reads

--split-files - Dump each read into separate file. Files will receive suffix corresponding to read number

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updated by Ram Ram • written by Evgeniia Golovina Evgeniia Golovina

--split-spot created just one file.

I tried --split-3, it gave 3 file:

SRR1652430_1.fastq, SRR1652430_2.fastq for paired ends, and SRR1652430.fastq for single reads.

But I'm not sure if it's the right way or not.

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updated by Ram Ram • written by rimjhim.roy.ch rimjhim.roy.ch

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