fastq-dump download pair-end fastq without split-files

Question

[Shicheng Guo]

Hey All,

What should I do if I forget to add the option of split-files in fastq-dump when I download pair-end fastq files from SRA database?

For example:

fastq-dump -X 20 SRR390728
fastq-dump --split-files  -X 20 SRR390728 
fastq-dump --split-3  -X 20 SRR390728

Answer 1

[GenoMax]

Re-do fastq-dump or get the fastq from ENA here

Answer 2

[Shicheng Guo]

Yes. I think actually it can be easily split each read to two part (SRA merge two 110bp reads to one 220bp reads). However, I change my mind, I re-download it with another way which can keep the fastq file of same sample in a fold so that I can alignment and merge the bam file easily.

wget -r -c -l 2 -nH --cut-dirs=4 ftp://ftp.ddbj.nig.ac.jp/ddbj_database/dra/fastq/SRA112/SRA112056/

of course, it also can be re-download with the command:

fastq-dump --split-files  --skip-technical SRR390728 
fastq-dump --split-files  --skip-technical SRR390729
fastq-dump --split-files  --skip-technical SRR390730

[Nelo]

what is the importance of --skip-technical option

Can we just use simply fastq-dump --split-files with SRA-ID

[GenoMax]

Yes you can. --skip-tech is likely a leftover from early days of SRA see: fastq-dump split-spot and skip-technical