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coverage RNAseq
I would like to determine the coverage of mapped reads in exons, introns and intergenic regions.
Are there tools that could help me?
Thanks
Are there tools that could help me?
Thanks
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Do you have access to any commercial programs? ParTek will generate such a summary report, after indexing to Refseq, Ensembl or AceView transcripts (or a custom annotation that you create).
You should also be able to do this with bedtools and you could use UCSC Genome Table Browser to get the appropriate regions as BED files. If you select, for example, "knownGene" and give your output a file name, then click "get output" you will go to a screen where you can select exons, introns, and so forth.
bedtools includes a "coverageBed" tool (compare one BED file of reads to another you've created from the UCSC Table Browser) and "complementBed" could be used to get the intergenic regions.
I've not used bedtools for this though, since I have a Partek license, I went with that.Michael Black, Ph.D.
ScitoVation LLC. RTP, N.C.
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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