Entering edit mode
6 months ago
DN99
▴
20
I have downloaded the bed.gz file from here: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE215727 (which comes from: https://www.encodeproject.org/experiments/ENCSR769DGC/)
The file's contents look like:
0 1 2 3 4 5 6 7 \
0 chr3 93470283 93470874 . 1000 . 23.42818 12894.75781
1 chr1 629080 630079 . 1000 . 5.52786 6997.08838
2 chr17 22521276 22521641 . 1000 . 43.79663 6201.15332
3 chr1 633839 634276 . 1000 . 4.61704 4971.29053
4 chrUn_KI270467v1 1877 3861 . 1000 . 7.89329 4170.91846
8 9 10 11 12 13 14 15 16 \
0 12887.15918 207 5.0 5.0 93470284 93470874 6462.64355 206 93470283
1 6990.22363 733 5.0 5.0 629083 630079 3545.76758 722 629078
2 6194.40332 130 5.0 5.0 22521276 22521641 3118.46362 130 22521277
3 4964.67236 169 5.0 5.0 633837 634275 2430.92163 171 633843
4 4164.42969 450 5.0 5.0 1877 3861 2034.28186 450 1898
17 18 19
0 93470874 6435.64404 207
1 630078 3540.59131 744
2 22521636 3055.09912 128
3 634275 2527.61523 164
4 3861 2139.85400 429
I am trying to figure out which column is the peaks data - I just need the chrom, start end and peaks columns.
However, I can't find any description file for these columns - how can I find out which column is which?
You will probably find your answer in these two links:-
https://github.com/nboley/idr
https://biodatascience.github.io/compbio/test/IDR.html
The first three columns are chr, start and end to me.