Get SRA file read number easily

Question

[Hojn]

Hi,

I have a question that might sounds weird but I don't have "easy" way to achieve it. I have conducted SRA download to get a list of SRR, which I then converted into fastq1 et fastq2 (fow and rev). However, I haven't thought about writing the process output in a file, thus I just lost reads information. I can retrieve reads number on the project BUT I have to manually click on each SRR file and then on "reads" information. Since I have 354 SRR files, this manipulation isn't worth. I want to compute all the reads number to compare with my fastq1 and fastq2 reads number to assess I haven't lost some during the process.

I have thought about making a Perl script to load each page-related SRR information but can't achieve it in this way, OR print all SRR content and | grep "@" | wc -l for each of them, BUT it's totally time-consuming.

Would you have a simple way to do so?

Thank you in advance!

Answer 1

[GenoMax]

You can use EntrezDirect to get the number of reads in a particular accession:

$ esearch -db sra -query SRR5134861 | efetch -format runinfo | cut -d "," -f4
spots
50658231

[Hojn]

Thank you for your response! I had read that spots number and reads number aren't substiantially the same thing. However, comparing now, it seems to be the same. I'll execute your command, thanks!