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Eland format to Bed format?
Dear all,
Sorry for my ignorance.. I wanted to get a simple bed file out of this data. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM353644 . But I don't know how to deal with this data. My question is could you help me out for changing the format of this data to Bed.
Here is the format of the GSM353644_jy10s123.allregions.txt data. As I understand from the 1s. they are chr number. I assume col 2 and 3 are start and end but I don't get what are the rest. I can to the formatting. I only need the information that which values are the equivalent of peak height? Thank you for your help
1 516326 516600 275 27 516512
1 740876 741050 175 11 740900
1 941326 941675 350 12 941537
1 1049026 1049275 250 8 1049212
1 1079126 1079475 350 29 1079300
1 1158776 1159025 250 10 1158862
1 1162801 1163000 200 9 1162912
1 1207001 1207200 200 10 1207087
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morovatunc
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morovatunc
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I believe this is already a BED-formatted text file and the scores for the peaks are in the fifth column. These peaks are called using HPeak and in their documentation they state:
.allregions.txt: This is the old main output file (in version 1.0 and 1.1). It is in BED format (no strand) indicating chromosome, start and end location, and the length (in bp) of all enriched regions. The fifth column contains the maximum coverage among all bins in this region. The last column indicates the normalized cumulative log transformed posterior probability of being ChIP-enriched. Note that the first column only contains the chromosome number, and X and Y are replaced by 23 and 24 for easier numerical manipulations.
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Gungor Budak
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Gungor Budak
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