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2.7 years ago
Ankita
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70
How to Download a single sample from ENA/SRA for Whole Exome Sequencing platform (e.g. SRR)
Convert the Raw format for sample to VCF (both somatic and germline mutations) using simple python code or R CODE OR ANY.
I dont think you can do that with any single line of code. Since the sequence is submitted in raw format, You have to download, perform alignment and process the samples manually according to the reads.
If you manage how to download SRR file (fastq), you can do the analysis without any coding by using public/ published workflows on Galaxy and an example WES workflow is here (https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html). Please read the manual or search on google how to download files from SRA/ENA. There are plenty of tutorials and automated scripts to address your query on downloading files from ENA/SRA. If you have preliminary coding experience, I would suggest to use either NF core prebuilt workflows or snakemake prebuilt workflows.
You can download files directly to Galaxy from the ENA Browser. e.g. Go to https://www.ebi.ac.uk/ena/browser/view/SRR212430?show=reads Click on "Show Column Selection" and check "fastq_galaxy" (assuming it's the generated fastq file you want) "Generated FASTQ files: Galaxy" column will now be visible in the table below. Click on a link in this column to start a download to Galaxy.