Hi everybody,
I'm analyzing iCLIP data (technique to study protein-RNA interactions on a genome-wide scale). I have two populations bound by the protein of interest - small RNA and mRNA.
I take all reads that map uniquely to the genome and i wanted to know all transcript that are bound by our protein of interest.
But i have a problem, i use bowtie to map unique mapper reads on the genome tothe transcriptome, but unique mapper on the genome became multi mapper on transcriptome, i'm confused, how to deal with it ? I have some very small reads ( the smallest are 13 nt).
How can i assign reads to transcript without mistake, i mean how to deal with reads aligning to multiple genes ?
do i have to associate each read with all transcripts it aligns to?
Thanks in advance for your help.
I'm analyzing iCLIP data (technique to study protein-RNA interactions on a genome-wide scale). I have two populations bound by the protein of interest - small RNA and mRNA.
I take all reads that map uniquely to the genome and i wanted to know all transcript that are bound by our protein of interest.
But i have a problem, i use bowtie to map unique mapper reads on the genome tothe transcriptome, but unique mapper on the genome became multi mapper on transcriptome, i'm confused, how to deal with it ? I have some very small reads ( the smallest are 13 nt).
How can i assign reads to transcript without mistake, i mean how to deal with reads aligning to multiple genes ?
do i have to associate each read with all transcripts it aligns to?
Thanks in advance for your help.
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