Submitting Unchaste Reads To Geo

Question

[Madelaine Gogol]

For illumina sequence data, GEO advises submitting all reads (including those that fail the chastity filter).

We weren't planning on continuing to save these reads, but we could if it's really necessary. We haven't been using them in our analysis.

Have you used such reads, and if so, how?

[David Quigley]

+1 for using the tag "chastity" in context.

Answer 1

[seidel]

I presume that GEO wants whatever you started your analysis with, so that others can reproduce, investigate, or extend the results. Almost all of my analyses begin with those reads already removed from the fastq files. So I have no qualms about submitting the fastq files I started with.

I think the key word is "necessary". If your conclusions depend on them (hard for me to imagine), and you used them in your analysis, they should be there. Otherwise if they were filtered out at some early step (perhaps before you even receive the data), they served no purpose in the analysis, and I think it's acceptable to omit them.

[Madelaine Gogol]

Okay, sounds good. How about someone whose office I can't see. LOL.

GEO via email advised us to keep all the reads in there. But they don't officially require it.