Hello!
I'm working in ChIP-Seq analysis of transcription factors using Illumina sequencing. After mapping (ELAND) and peak finding (FindPeaks - Thanks to Anthony!!!) i'm happy to have the coordinates of potential binding sites.
Now i’m interested in placing the peaks into genomic context in the form of intergenic regions, genes, intros, exons, promoters and so one with reference to the human genome (or RefSeq genes..). Can anyone recommend a tool or something to manage this question?
Furthermore is there any recommendation for an automated output of the sequence from the start to the end coordinate of the identified peaks in order to look for consensus motifs inside the peaks?
Best regards!
tec
I'm working in ChIP-Seq analysis of transcription factors using Illumina sequencing. After mapping (ELAND) and peak finding (FindPeaks - Thanks to Anthony!!!) i'm happy to have the coordinates of potential binding sites.
Now i’m interested in placing the peaks into genomic context in the form of intergenic regions, genes, intros, exons, promoters and so one with reference to the human genome (or RefSeq genes..). Can anyone recommend a tool or something to manage this question?
Furthermore is there any recommendation for an automated output of the sequence from the start to the end coordinate of the identified peaks in order to look for consensus motifs inside the peaks?
Best regards!
tec
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