I am a research tech in a wildlife genetics group and my PI and I are trying to figure out how/where to put raw reads in a repository. We have capture-seq NGS from Rapid Genomics. The post-doc who was working on a project left our lab group and has not been in good communication to assist. I am new to working with NGS data, slowly trying to figure it out! Any input would be very appreciated!
Maggie
In the case of model organisms, the gene expression omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/info/submission.html) is a commonly used repository to deposit sequencing data. I suspect it is the case for other organisms as well.
Hi Magdalena,
If you have raw fastq reads you can simply upload your data on SRA (https://www.ncbi.nlm.nih.gov/sra), it's where ALL the NGS data is uploaded on NCBI.
I'm not sure you can upload on GEO because it accepts studies concerning differential gene expression and regulation, epigenetics, or other functional genomic studies. I'm not familiar with CaptureSeq but it is basically a targeted genome resequencing so you check genotypes, SNPs etc... right?
If that's the case you should create a BioProject for your experiment on SRA (the bioproject is basically a "folder" containing all the reads you produced for a specific experiment/project/manuscript) and then upload your reads in the bioproject, here is the guide: https://www.ncbi.nlm.nih.gov/sra/docs/submit/#submitting-via-sra-submission-po
It's pretty easy, the only complicated part may be the actual uplod of the file. I suggest you to use FileZilla to transfer the files by FTP. Anyway, you find the instrunctions on their websites.
If you have any doubt you can contact the SRA team, they're really nice and helpful!
Best
Umberto
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