SRA: fastq-dump gives different number of sequences

Question

[jeetsahu]

I have downloaded read sequences using fastq-dump with split file option and SRR id for paired sequences. But splitted files have different number of sequence reads. As per my understanding, since these are paired-end reads these should have equal number of sequences.

$fastq-dump -I --split-files SRR390728

$grep -c '>' SRR7716545_1.fastq

694067

$grep -c '>' SRR7716545_2.fastq

1026976

Please correct me if I am wrong.

Answer 1

[ATpoint]

Both files have the same number of reads. You have to grep for '^@', because @ is the fastq header prefix. > is fasta.

ls *.fastq | parallel "echo {} && grep -c '^@' {}"
SRR7716545_1.fastq
5644111
SRR7716545_2.fastq
5644111

[jeetsahu]

Thanks, I grepped different symbol. One quick question - Does fastq-dump gives latest dataset used for assembly? if yes how can I get old datasets?

[ATpoint]

fastq-dump gives the fastq based on the input SRR you give it. I have no detail knowledge about your SRR.

[finswimmer]

Hello jeetsahu ,

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