Question: How to determine RNA-seq samples from dbGaP metadata
gravatar for komal.rathi
11 months ago by
Children's Hospital of Philadelphia, Philadelphia, PA
komal.rathi3.4k wrote:

Hi everyone,

I have dbGaP metadata for a project that has multiple datatypes (WES, WGS, RNA-seq etc) and I am trying to select only samples corresponding to RNA-seq but I am quite confused looking at a few columns in the metadata. Here are the columns:

> plyr::count(dat[,c('Assay_Type_s','analyte_type_s','molecular_data_type_s')])

  Assay_Type_s analyte_type_s molecular_data_type_s freq
1      RNA-Seq            DNA        <not provided>    1
2      RNA-Seq            RNA        <not provided>  309
3      RNA-Seq            RNA           miRNA (NGS)  150
4      RNA-Seq            RNA         RNA Seq (NGS)  324
5      RNA-Seq            RNA  Targeted Exome (NGS)   32
6      RNA-Seq            RNA     Whole Exome (NGS)    4
7      RNA-Seq            RNA    Whole Genome (NGS)   62

Here, as you can see the Assay Type is RNA-Seq but then you also see Analyte Type as DNA or RNA and Molecular Data Type as either miRNA, RNA-Seq, Targeted, Whole Exome and Whole Genome. How is the relationship determined between these columns and which samples would really be from a RNA-seq experiment?


dbgap metadata • 378 views
ADD COMMENTlink modified 11 months ago by Santosh Anand4.9k • written 11 months ago by komal.rathi3.4k
gravatar for Santosh Anand
11 months ago by
Santosh Anand4.9k
Santosh Anand4.9k wrote:

My guess is that the Exome related stuffs refer to Exome Capture RNAseq

The key point is "degraded samples" where RNA cant be captured by usual ribo-zero or polyA (see paper above)

This is also evident from the description of data types

I have no idea about the 1st sample (DNA), though it could be an error also given the fact that there is only one sample of that kind.

ADD COMMENTlink written 11 months ago by Santosh Anand4.9k

I don't get it. My question is what are those samples with Molecular Data Type != RNA Seq (NGS)? Are those also RNA-sequencing? If not, then why is the Assay Type = RNA-Seq?

ADD REPLYlink written 11 months ago by komal.rathi3.4k

Check the paper, you'll get the idea.

"...Unique to capture transcriptomes is an overnight capture reaction (RNA-DNA hybridization) using exon-targeting RNA probes, followed by a washing step, and an additional set of PCR cycles..."

ADD REPLYlink written 11 months ago by Santosh Anand4.9k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1512 users visited in the last hour