Universal Human Reference RNA Sample

Question

[kstangline]

Does anyone know where I can find a Universal Human Reference RNA sample? Bam, fastq, or anything that is publicly available?

In other words, something like this that is publicly available to download:

https://www.thermofisher.com/order/catalog/product/QS0639#/QS0639

Answer 1

[michael.j.apostolides]

I believe here: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP025982

They are from the SEQC https://www-nature-com.proxy3.library.mcgill.ca/articles/nbt.2957

I filtered for platform=ILLUMINA, organism=Homo sapiens, Sample= A (UHRR)

https://www.ncbi.nlm.nih.gov/Traces/study/?acc=SRP025982&f=platform_s%3An%3Aillumina%3Borganism_s%3An%3Ahomo%2520sapiens%3Bseqc_sample_sam_s%3An%3Aa%3Ac&o=acc_s%3Aa

There are so many runs here, from different dates and sequencingcenters. I guess you can just choose one or some of them

[michael.j.apostolides]

For example you can see it here, this is the first one in the table (SRR1215996):

https://trace.ncbi.nlm.nih.gov/Traces/index.html?view=run_browser&acc=SRR1215996&display=metadata

Then you can do the following:

#!/bin/bash

module load sratoolkit

prefetch ${SRA_ID}  --max-size 100G --output-directory ${ILLUMINA_DIR} > ${ILLUMINA_DIR}/logs/${SRA_ID}.prefetch.log

fasterq-dump --split-files ${SRA_ID}

# You will get the following output from your command:
#spots read      : 10,934,900
#reads read      : 21,869,800
#reads written   : 21,869,800

Your fastq file will be called SRR1215996_1.fastq and SRR1215996_2.fastq