BED files for SRA open projects

Question

[ognjen011]

Hello!

I apologize in advance if this is not something that should go to the knowledge base, but I keep hitting a similar wall in analyzing FASTQ files on SRA that are open to public. When dealing with exome data I keep having trouble finding the information which capture kit is used, especially if the paper is hidden behind a subscription (Which it often is). When I do find out which capture kit was used, I have trouble finding the BED file.

For example, I found out a project used Qiagen Qiaamp DNA Mini kit. I registered with the website and went all over the internet, but I haven't found any BED files, or any resources that explain their acquisition. Customer support is ignoring me, possibly because it is a silly question. In general, how does one find these BED files and why are they not public?

Thanks in advance!

Answer 1

[ATpoint]

The Qiaamp is a DNA purification kit, it does not do any target enrichment. Therefore, customer service is probably ignoring you, as the question does not make sense. I would check the GEO entry of the respective SRA if there are any information given in the methods section. Still, the methods section in the publication must provide this information. Why are many journals not public...well because capitalism. How many publications would you need to check?

EDIT: As pointed out below, I was mixing up GEO and SRA. It is not GEO to check for details, but rather the SRA portal. GEO does not accept WES/WGS data, but some DNA samples such as ChIP-seq.

[ognjen011]

Thanks, it makes sense now. I got second hand info on the capture kit as I couldn't see the supplementary. Thanks for the clarification on the purification kit.

Can you explain more on the "GEO entry of the respective SRA"? This is a DNA sample, so I am not sure if it can be found in GEO. For the current sample these is nothing on methods.

[GenoMax]

GEO accepts certain kinds of high throughput sequence data and you are right that DNA sequencing is not one of them.

It is partly the submitters fault that they (sometimes) do not provide complete metadata requested by GEO/SRA. In that case your only recourse is to look through the publication if you can find out the type of kit used or failing that contact the authors.