I have many SRA accession numbers and I need to download the fastq files. I am using fastq-dump command to download the fastq files in the Linux system but it works for a single accession number. I have many accession numbers for which fastq files are to be downloaded.
To download multiple FASTQ files using `fastq-dump` in a Linux system, you can create a list of accession numbers or SRA IDs for the files you want to download and use a loop to download them one by one. Here's an example:
1. Create a text file named `accessions.txt` and list the accession numbers or SRA IDs, one per line:
```
SRR1234567
SRR1234568
SRR1234569
```
2. Open a terminal window and navigate to the directory where you want to save the FASTQ files.
3. Use the following command to download the files:
```
while read line; do fastq-dump $line; done < accessions.txt
```
This command reads the `accessions.txt` file line by line and runs `fastq-dump` on each accession number. The resulting FASTQ files will be downloaded to the current directory.
You can modify the command to specify additional options, such as the output directory or the number of threads to use for downloading. For example:
```
while read line; do fastq-dump --outdir /path/to/output --split-files --threads 4 $line; done < accessions.txt
```
This command downloads the FASTQ files to the `/path/to/output` directory, splits paired-end reads into separate files, and uses 4 threads for downloading.
Hope it helps!
Credit: mainly to AI
Hi Saesha Verma
Follow this few steps
First open terminal in the directory you wish to download the files, and make sure you have read/write access to it.
Now create a text file with a desirable name say num.txt and with all the SRA accession numbers.
Save the file and run the following command
cat num.txt | xargs -n 1 fastq-dump
Hope it helps
Mohammad Imam thank you for your answer. As I use this command "while read line; do fastq-dump $line; done < List1.txt" gives me the output "bash: List1.txt: No such file or directory.
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