I am using BedTools Map operation to map the DNAse I signal of a cell type into some chromosome regions, by computing the mean on the third column
The command I use is the following:
$ bedtools map -a inputFile1.bed -b inputFile2.bedgraph -c 4 -o mean 1> outputFile
In the output file, I have real value for chrom1 -> chrom9, but strangely I find all dots for the other chromosome regions:
chr1 66660 66810 0.849999999999999977796
chr1 87640 87790 0.0500000000000000027756
chr1 96520 96670 0
chr1 115600 115750 115.527272727272702468
chr1 118840 118990 3.10000000000000008882
chr1 125340 125490 0
chr1 136280 136430 .
chr1 136960 137110 .
chr1 235600 235750 39.0559633027522963289
chr1 237020 237170 1.59999999999999986677
.... .... .... ....
.... .... .... ....
.... .... .... ....
chr10 134874600 134874750 .
chr10 134876820 134876970 .
chr10 134877940 134878090 .
chr10 134878160 134878310 .
chr10 134879420 134879570 .
chr10 134897500 134897650 .
chr10 134907140 134907290 .
chr10 134915640 134915790 .
chr10 134939120 134939270 .
chr10 134939280 134939430 .
chr10 134940860 134941010 .
.... .... .... .... .... ....
Do you know why this strange behavior happens?
Why don't I have all the values for chrom10...19, too?
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written
by
Davide Chicco
See option -null http://bedtools.readthedocs.org/en/latest/content/tools/map.html
-null The value to print if no overlaps are found for an A interval. Default: "."
Thanks Pierre, but it's not that case. Overlaps are present, at least for some regions. It just put dots for ALL, and I cannot understand why....
Thanks to Brentp that suggested me to use the command cut -f 1 fileName1.bed | uniq -c, I noticed that the two chromosome region files were sorted in different order.
This first file was sorted alphanumerically: chr1, chr2 , chr3, ..., chr9, chr10, chr11, ...
Conversely, the second file was sorted alphabetically: chr1, chr10, chr11, ..., chr19, chr2, chr20, chr21, ...
This inconsistency between these two files messed up the BedTools Map operation. To solve this, I simply sorted alphabetically the first file, too. I used the Linux command: sort -k1,1 -k2n file > sortedFile
Merci Pierre!
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written
by
Davide Chicco
I am glad you were able to sort this out. We are working on enhancements that will (in most cases, not all) detect inconsistent sorting rules and throw an error to alert the user. Hoping to have it out in the next release.
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written
by
Aaronquinlan
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sounds like a sorting problem. what are the outputs of:
you may need to sort one of them.
Output of the first:
Output of the second:
Any clue?
yes, a sorting problem. sort both with
sort -k1,1 -k2,2n $bed