annotate and analyse mutation from cosmic

Question

[sahhomaha]

Hi, I want to know the pipline aboout: how can I download and analyse mutations from cosmic cancer cataloge , and how can I get output that can help to intersect it with TFchip seq. data of breast cancer cell line! I am completley new in the bioinformatics and I do need adivice, Thank you

Answer 1

[manuel.belmadani]

You can download the COSMIC mutations from the COSMIC download page. Get the VCF format files from "VCF Files (coding and non-coding mutations)". VCF files are "variant calling" files, meaning they contain variant (mutation) positions and annotations.

Your TF ChIP-Seq data may be formatted in BED format, which is simply a file with a chromosome and coordinate ranges. For ChIP-Seq, these typically represent the called peaks where TF binding is suspected. If your data/peaks aren't in BED format already, it's easy to make one by making a tab-separated file of chromosome, start of the peak, and end of the peak (read the UCSC link on BED files first.) You can get more BED files of ChIP-Seq like this from ENCODE.

Install bedtools and use bedtools intersect to find the intersection between your VCF and BED file.

bedtools intersect [OPTIONS] -a <FILE> \
                             -b <FILE1, FILE2, ..., FILEN>

The output should be a filtered COSMIC VCF with only mutations intersecting your peaks.