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We have a mapped RNA-seq but now we want to know how many reads are mapped on each nucleotide in a genome. We went through many many many programs but we were only able to view the results in no scientific way. I was wondering is there any?
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Dear pal,
you can use BED tools to find coverage per nucleotide. -
Hello,
Thanks for the reply, you mean using coverageBed?
Am now at the positiion of coverageBed -a bedfile.bed but the tutorial talks about 10kb? how to do this for each nucleotide? Sorry for the questions...
** Got it... ill write an explanation soon! Thanks alot udaya! **Last edited by jjk; 10-03-2011, 03:05 AM.Comment
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samtools pileup has this infoMendelian Disorder: A blogshare of random useful information for general public consumption. [Blog]
Breakway: A Program to Identify Structural Variations in Genomic Data [Website] [Forum Post]
Projects: U87MG whole genome sequence [Website] [Paper]Comment
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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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