Question

Number and percent of mapped reads from RNA seq analysis.

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Anthony Nash ▴ 20

@anthony-nash-17385

Last seen 5.8 years ago

University of Oxford

Sorry if this is a simple question for some, I am flying blind on my first attempt at RNA seq with a demand for immediate deadlines.

I've used a process of Salmon (with FASTQC) -> tximport -> DESeq2 and I've thrown in a bit of Scater for some PCA calculations. however, I would like to plot the absolute number and percent of mapped reads to each experimental sample (6 controls, 6 exposures). Given the above workflow, is there anything available to yield this information?

Thanks

rna-seq rna • 1.6k views

ADD COMMENT • link updated 5.8 years ago by Steve Lianoglou ★ 13k • written 5.8 years ago by Anthony Nash ▴ 20

score 0 · Answer 1 · 2019-03-27

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Steve Lianoglou ★ 13k

@steve-lianoglou-2771

Last seen 22 months ago

United States

Since you're just getting started in the RNA-seq world, it wouldn't hurt to read up on the multitude of tools that MultiQC works with.

The example report right under the fold when you start scrolling down is probably exactly what you want.

Now you just have to figure out how to get MultiQC up and running with your setup, which shouldn't be a stretch too far as it's got a fair bit of documentation.

Good luck!

ADD COMMENT • link 5.8 years ago Steve Lianoglou ★ 13k

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Isn't there a tool within Bioconductor suite that can do this rather than adding in further software?

ADD REPLY • link 5.8 years ago Anthony Nash ▴ 20

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To get the percentages, you need to know the number of total reads, which so far as I know salmon doesn't report. So you need to count the total number of reads in each FASTQ file by either reading each in using something like readFastq in the ShortRead package, or by using a system call like zcat fastq.gz | wc -l and capturing the output (or maybe some other way that isn't occurring to me at this point), or by using MultiQC, which will collate the total number of reads into a nice table that you can read in using read.delim.

I tend to use MultiQC, because it generates a really nice HTML page showing the collated QC data from FASTQC, and as a side effect gives me the total counts. So two birds, one stone.

ADD REPLY • link 5.8 years ago James W. MacDonald 67k