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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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