Overlap With Known Gene Models

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12.9 years ago

Steffi ▴ 580

Hi,

I just mapped public data (dtbio from the nagalakshmi paper, rna seq, yeast). Let's say I can map 1 million reads with bowtie to the genome. Out of this one million reads just about the half overlap with known genes. How can this be? As far as I know there is not so much splicing in Yeast, so where do all these reads derive from?

looking forward to your answers, steffi

rna gene • 2.4k views

ADD COMMENT • link updated 10.9 years ago by Biostar 20 • written 12.9 years ago by Steffi ▴ 580

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Does the paper give any statistics on how many reads map to known genes, or genomic regions not in current gene models? How did those authors align their reads to known genes - via the genome and checking coordinates for overlap with known genes, or to cDNA (RefSeq) seqs of known gene models? In other words, let's compare your method to theirs.

ADD REPLY • link 12.9 years ago by Larry_Parnell 16k

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@Steffi: Please add the link to the rna seq paper.

ADD REPLY • link 12.9 years ago by Khader Shameer 18k

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This is similar to the mapping in the paper (56% unique mappings, 60% total).

ADD REPLY • link 12.9 years ago by Oligo ▴ 60

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