Chromosome Coordinates

Question

[wdaali99]

I have a MeDIP-seq reads for each chromosome and the resolution is 100 bp. My questions is how can I plot my read counts vs genes of interests. From USCS browser, I can get location of these genes and their coordinate on the chromosome. Take for example data on chr1, it looks like this: 0 0 20 0 0 35 0 0 ......... Counts are recorded after each 100 base pair. But I dont know how to map my read counts to chromosome coordinates.

I'm new to this field and any help or suggestion will be greatly appreciated!

Amy-

Answer 1

[Giovanni M Dall'Olio]

You have a file containing the gene coordinates, and another file containing your MeDIP-seq reads.

A possible solution is to convert both files to the BED format, and then use intersectBed from bedtools to merge the two.

Example input genes file:

chr7    1000    1500    gene1   0   +
chr7    2000    2500    gene2   0   +
chr7    4000    5000    gene3   0   +
chr7    6000    7000    gene4   0   +

Example input MeDIP-seq reads count file:

chr7    1000    1001    sc  10  +
chr7    1100    1101    sc  10  +
chr7    1200    1201    sc  2   +
chr7    1300    1301    sc  10  +
chr7    1400    1401    sc  1   +
chr7    1500    1501    sc  10  +
chr7    1600    1601    sc  0   +
chr7    1700    1701    sc  10  +
chr7    1900    1901    sc  10  +
chr7    2000    2001    sc  10  +
chr7    2100    2101    sc  10  +
chr7    2200    2201    sc  10  +
chr7    2300    2301    sc  10  +
chr7    2400    2401    sc  10  +
chr7    2500    2501    sc  10  +
chr7    2600    2601    sc  10  +

Example of merged bed file (use the options -wa and -wb):

$: intersectBed -a bedseqscount.bed -b bed_genes.bed -wa -wb

chr7    1000    1001    sc  10  +   chr7    1000    1500    gene1   0   +
chr7    1100    1101    sc  10  +   chr7    1000    1500    gene1   0   +
chr7    1200    1201    sc  2   +   chr7    1000    1500    gene1   0   +
chr7    1300    1301    sc  10  +   chr7    1000    1500    gene1   0   +
chr7    1400    1401    sc  1   +   chr7    1000    1500    gene1   0   +
chr7    2000    2001    sc  10  +   chr7    2000    2500    gene2   0   +
chr7    2100    2101    sc  10  +   chr7    2000    2500    gene2   0   +
chr7    2200    2201    sc  10  +   chr7    2000    2500    gene2   0   +
chr7    2300    2301    sc  10  +   chr7    2000    2500    gene2   0   +
chr7    2400    2401    sc  10  +   chr7    2000    2500    gene2   0   +

From this file you can easily calculate the sum of values per each gene. There are many ways to do it, for example the doBy library in R.

[wdaali99]

Thank you so much for your help. How can I convert .txt file to .BED format with delimited columns? is there a way I can do it in Matlab?

best, Amy

[Giovanni M Dall'Olio]

You'll have to write a script to do it. I can't help you more because I don't know how your txt file looks like. If you want help, you should better open a new question and show an example of how your txt file looks like.