Question: How to calculate the average of mapping coverage?
0
gravatar for seta
2.5 years ago by
seta1.1k
Sweden
seta1.1k wrote:

Hi all,

I did de novo transcriptome assembly using paired-end reads from Illumina Hiseq 2000 for a non-model organism. I mapped back reads to transcriptome assembly. If I'm not wrong, the average of mapping coverage shows the read number (in average) that mapped to each reconstructed transcript (contig). Could you please let me know if this number is important and why? and how I can calculate it?

Thank you for your answer

ADD COMMENTlink written 2.5 years ago by seta1.1k

From Biostar Handbook. Genome/Chromosome size in your case will be the size of the contigs.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax65k

Are you sure? As I found on the net, the people used bedtools for it, however, I'm not sure about mapping read to de novo assembled transcriptome? Any suggestion

ADD REPLYlink written 2.5 years ago by seta1.1k

If the newly assembled transcriptome is your "reference" then that is what you have. You would expect a large % of the original reads to map to this new reference/transcriptome (if they don't then you probably have a bad assembly or some other issue). So unless you have a real reference available you can calculate coverage taking into account the contigs you now have in the new assembly.

ADD REPLYlink written 2.5 years ago by genomax65k

Thank you. I found this paper enter link description here and more confused with reading the "Transcript quantitation, coverage and depth analysis" section. Sorry, could you please kindly tell me what is the story and the importance of this calculation (coverage and depth analysis)?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by seta1.1k

How to calculate can be easily found in the manual @genomax2 post,
more can be found here
How To Calculate Coverage
Tools To Calculate Average Coverage For A Bam File?

regarding why if you have wrong assembly they will not map right

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Medhat8.2k

Thank you. I read the post that you mentioned before posting the question here, however, there were lots of options so I'm confused as this is my first experience. Regarding why, I know high mapping percentage, especially proper read mapping for PE reads, is indicative of a good assembly, but, my mean is which concept can be extracted from this number (average of mapping coverage)?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by seta1.1k

I think for me bedtools or GATK DepthOfCoverage will do the job for you

ADD REPLYlink written 2.5 years ago by Medhat8.2k
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