Hi all,
I am dealing with ChIP-seq data for a small lung cancer sample. The genomic sequences of this cancer sample is available in this paper: "A small-cell lung cancer genome with complex signatures of tobacco exposure". We are trying to build a specific reference genome based on the whole genome sequences provided in this paper and map our ChIP-seq data back to this specific reference genome.
My problem is that the gene annotation files like GTF files will be very different for this specific reference genome and common reference genome (Hg19), because of the somatic variation (insertions, deletions, rearrangements) in this cancer genome. The coordinates for transcripts will change a lot. Is there a software of program to solve this problem?
Something like by providing hg19 GTF files and information for all somatic variations as listed in this link, it can output a gene annotation file for this specific cancer reference genome.
or if not, could someone give a clue about how to cleverly do that?
Thanks a lot!
I am dealing with ChIP-seq data for a small lung cancer sample. The genomic sequences of this cancer sample is available in this paper: "A small-cell lung cancer genome with complex signatures of tobacco exposure". We are trying to build a specific reference genome based on the whole genome sequences provided in this paper and map our ChIP-seq data back to this specific reference genome.
My problem is that the gene annotation files like GTF files will be very different for this specific reference genome and common reference genome (Hg19), because of the somatic variation (insertions, deletions, rearrangements) in this cancer genome. The coordinates for transcripts will change a lot. Is there a software of program to solve this problem?
Something like by providing hg19 GTF files and information for all somatic variations as listed in this link, it can output a gene annotation file for this specific cancer reference genome.
or if not, could someone give a clue about how to cleverly do that?
Thanks a lot!
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