Hello, I'm a student who hasn't done much analysis before. I would appreciate it if you could understand even if my question is somewhat basic. I wanted to perform quality control, adapter trimming, mapping, and quantification on the raw data from a dataset available on GEO. I downloaded all the data from the SRA of SRP074349 within the GSE81089 dataset. However, I noticed that there are multiple SRRs (runs) for several SRXs (experiments).
In this case, should I choose only one, merge them into one, or filter them using FastQC or similar tools? I'm curious about the best approach.
1 answer
This is a large project (670 samples) and you can get a better look at the sample metadata using SRA Run selector: https://www.ncbi.nlm.nih.gov/Traces/study/?query_key=1&WebEnv=MCID_6464a81284083773086ece4b&o=sample_name_s%3Ad%3Bacc_s%3Aa
If you sort the table by "Sample Name" you will see that there are some samples with multiple SRA numbers. These are more than likely technical replicates that can be merged into one at some point in data processing.
But for others you will want to check the metadata to see if metadata distinguishes them e.g. tumor/normal from same patient.
Log in to answer this question.
-
How to Process Multiple SRRs for the Same BioSample ?
written by omicon •
-
miRNAs - Adapters, adapters, adapters i´m so confused
written by omicon •
-
multiple response SRR URLs for the same service 's3'
written by akar_ozan01 •
-
How to handle more than 1 SRA Run per Experiment?
written by Janmajay •
-
Adaptor sequence not present in raw paired-end reads
written by Petesview •
-
Name for bulk-metagenomic studies?
written by pawhitesell •
-
How to proceed with multiple runs ChIP-seq
written by buffealo •
-
Analysis of RNA-seq data of Ion Torrent
written by Wang •
-
Tool: SRA sequnce, FastQC, RNA seeq
written by Rahul •
-
how to remove adapter sequence in RNAseq fastq file from a paper.
written by cfarmeri
