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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Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
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