How to download a sra file

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Montrez-moi un peu d'amour avec les like ci-dessous The file SRR After you have downloaded the SRA file, you can use the command fastq-dump to extract the contents of it into a. A sample command to extract SRR We observe that two fastq files have been extracted from SRR This is because the original data was produced from paired-end sequencing, which usually has both a Read1 file and Read2 file.

I typically use the settings provided above for fastq-dump as my default settings. Since there are lots of SRA files associated with our samples, it would take a long time to manually run prefetch and fastq-dump for all the files. To automate this process, I wrote a small script in python to first download each SRA file using prefetch and then run fastq-dump. I would advise against it, since I have found this method to be much slower than first running prefetch and then fastq-dump on the pre-downloaded SRA files.

Repost by indicating the source please! Almost all HTS data in published publications will be asked uploading to here, and stored as. Mostly, we download sra files for the purpose of getting corresponding fastq or sam files, so as to use them in our own pipeline for downstream analysis. If not, go to SRA database. Thanks for suggestions. True, but no gzip compression for splitted files :D at least not in the initial release.

Login before adding your answer. Use of this site constitutes acceptance of our User Agreement and Privacy Policy. Log In. Log In Sign Up About. Entering edit mode. Obi Griffith 19k. Hi, how do we put in a dbgap crendentials? I tried: prefetch -v SRR but I'm getting this error. How to download sra data for example SRP? Does it have problem? Without details on what problems you have it is impossible to help.

Can you please help me? I have used. What if I want to use fastq-dump to get the final 5 reads of this data?? Istvan Albert 90k. This line works really well, thank you! Thanks for adding this. I am very new in this fiels. You want to get them all?