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6 months ago
Jjbox ▴ 40

I am trying to calculate the depth coverage between short read and long read in rna-seq. Below screenshot is the output file, [prefix]_Log.final.out.

My understanding of calculating the coverage in short read is read_length #_aligned_reads which gives 88 36385382. But, when we say coverage, it's represented as 40 x (every base in the static length genome is covered 40 times with reads).

Any help would be appreciated how to get the coverage like x10 in short read and long read. First, how do you calculate coverage in short read based on the screenshot below?

short long read rna-seq • 516 views
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You will want to use a program that will calculate this instead of using this log file. One example

\$ samtools depth
Usage: samtools depth [options] in.bam [in.bam ...]


It may also be worth considering this: What exactly is sequencing depth in RNAseq?

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6 months ago

With RNA-Seq coverage has a different meaning as different transcripts are expressed at different levels.

When you have a randomly sheared DNA then the expected coverage is the total sequenced length divided by the target genome length

C = T/G


where T is the sum of all reads, if all reads are of the same length then T=N*L

now once you align the reads, you can apply various corrections; only the aligned reads should be counted with N, and only the average aligned length should be included as L, both will be smaller than theoretical.

IT does not matter that you have long or short reads, other than for long reads you have to sum up the reads into T

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Thank you Istvan! I also have another question regarding finding tools that generate realistic rna-seq reads. Could you take a look at this question too, please? Tools for generating realistic rna-seq reads