Seqanswers Leaderboard Ad
Collapse
Announcement
Collapse
No announcement yet.
X
-
Originally posted by drdoodlebug View PostThe SRA submission portal is driving me over the edge. I have a massively multiplexed 454 16s pyrotag run, do I really have to create a biosample for every one of my 100+ samples???
For the SRA metadata, they have a 5 sheet Excel document you can fill out for bulk submissions too. Just email sra@ncbi. They have been very helpful for our bulk (>100 sample) submissions.
Leave a comment:
-
The SRA submission portal is driving me over the edge. I have a massively multiplexed 454 16s pyrotag run, do I really have to create a biosample for every one of my 100+ samples??? Another question about naming objects, where does it ever end? I'm trying to put up a single run and I swear I've created a baker's dozen names for each step. There has to be a better system. I'm beginning to understand why I pull up American pubs that have their data deposited with EBI and DDBJ. Grrr!
Leave a comment:
-
It's good to see I am not the only one who gets confused with the SRA data model :-)
I tried to think of it as a tree, but it is really a forest/graph. We use the Study accession number in publications, but then we usually only have one Experiment.
How sure are you of the statement "A Study consists of a series of Experiments with unique Samples. The Experiment in turn, consists of a number of Runs." ?
I do know that a Run can contain multiple Samples. This occurs when you multiplex samples into a single lane on Illumina for example. The same Sample could also be in multiple Runs, say you sequence it with Illumina and 454. And so on.
Leave a comment:
-
SRA metadata structure
Hello,
We know from the SRA article in NAR that the SRA metadata model has 6 objects (http://www.oxfordjournals.org/nar/database/summary/1456)
i. Study – high level info e.g. goals of the study, literature references – may be linked to BioProject dbase
ii. Sample – may be linked to BioSample databases
iii. Experiment – library information; instrument information
iv. Run – library information; instrument information
v. Analysis – analysis results e.g. alignments, assemblies
vi. Submission – groups the other objects
And that: ‘A Study consists of a series of Experiments with unique Samples. The Experiment in turn, consists of a number of Runs.’
Our Big Question is:
What is the object of interest – what do people refer to – is it the experiment? The study? The run? We are interested in this because we are trying to map the data flows and so which object(s) should we be following?
We are also interested in:
useful diagrams or descriptions the way that the metadata in the SRA is structured, including the relationships between the metadata objects
Definitions of what a ‘run’ is.
Latest Articles
Collapse
-
by seqadmin
Next-generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR) are essential techniques for investigating the genome, transcriptome, and epigenome. In many cases, choosing the appropriate technique is straightforward, but in others, it can be more challenging to determine the most effective option. A simple distinction is that smaller, more focused projects are typically better suited for qPCR, while larger, more complex datasets benefit from NGS. However,...-
Channel: Articles
10-18-2024, 07:11 AM -
-
by seqadmin
Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.
Nobel Prize for MicroRNA Discovery
This week,...-
Channel: Articles
10-07-2024, 08:07 AM -
ad_right_rmr
Collapse
News
Collapse
Topics | Statistics | Last Post | ||
---|---|---|---|---|
Started by seqadmin, 11-01-2024, 06:09 AM
|
0 responses
21 views
0 likes
|
Last Post
by seqadmin
11-01-2024, 06:09 AM
|
||
New Model Aims to Explain Polygenic Diseases by Connecting Genomic Mutations and Regulatory Networks
by seqadmin
Started by seqadmin, 10-30-2024, 05:31 AM
|
0 responses
20 views
0 likes
|
Last Post
by seqadmin
10-30-2024, 05:31 AM
|
||
Started by seqadmin, 10-24-2024, 06:58 AM
|
0 responses
24 views
0 likes
|
Last Post
by seqadmin
10-24-2024, 06:58 AM
|
||
New AI Model Designs Synthetic DNA Switches for Targeted Gene Expression in Specific Cell Types
by seqadmin
Started by seqadmin, 10-23-2024, 08:43 AM
|
0 responses
53 views
0 likes
|
Last Post
by seqadmin
10-23-2024, 08:43 AM
|
Leave a comment: