How to find column names for ENCODE ATAC-seq data?
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9 days 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?

encode atac-seq bed • 221 views
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You will probably find your answer in these two links:-

https://github.com/nboley/idr

https://biodatascience.github.io/compbio/test/IDR.html

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The first three columns are chr, start and end to me.

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