Eland format to Bed format?
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6.0 years ago
morovatunc ▴ 510

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 dont 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 dont 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

 

ChIP-Seq GEO BED • 1.5k views
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6.0 years ago
Gungor Budak ▴ 250

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.

http://www.broadinstitute.org/~anshul/projects/encode/preprocessing/peakcalling/hpeak/HPeak-2.1/hpeaks2manual.pdf

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I brain METU. Thanks!

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