Question: fastq-dump download pair-end fastq without split-files
1
gravatar for Shicheng Guo
2.3 years ago by
Shicheng Guo4.9k
Shicheng Guo4.9k wrote:

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 

 

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Shicheng Guo4.9k
1
gravatar for Shicheng Guo
2.3 years ago by
Shicheng Guo4.9k
Shicheng Guo4.9k wrote:

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 

 

 

ADD COMMENTlink written 2.3 years ago by Shicheng Guo4.9k
0
gravatar for genomax
2.3 years ago by
genomax49k
United States
genomax49k wrote:

Re-do fastq-dump or get the fastq from ENA: http://www.ebi.ac.uk/ena/data/view/SRR390728

ADD COMMENTlink written 2.3 years ago by genomax49k
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