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Question: Find cooccurences of factors across multiple files
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gravatar for tirichl
9 weeks ago by
tirichl • 20
Wüzrburg
tirichl • 20 wrote:

Hey,

I have several hundred files that look like this:

a.file
#genomic positions
1, 3, 4, 9, 10
#factors
a, b, d, g

Each file holds multiple genomic positions (numbers) and factors (characters). I want to investigate, whether there are genomic positions that frequently co-occur with factors across all files, but I have no idea on how to approach this. Can someone point me into the right direction? Is there a tool or a library that might help? Thank you!
sequencing chip-seq gene • 113 views
ADD COMMENT • link •
modified 9 weeks ago by jordi.planells • 330 • written 9 weeks ago by tirichl • 20
0
gravatar for jordi.planells
9 weeks ago by
jordi.planells • 330
jordi.planells • 330 wrote:

bedtools intersect accepts multiple file to be intersected. Have you tried with it? You can report the number of occurrences with -c flag.

bedtools intersect -c -a your_file -b factor1 factor2 factorN

Then you could print the lines with more than X occurrences with awk.

awk 'BEGIN{FS="\t";OFS="\t"}{if($4 > X) print $0}'

Hope it helps!
ADD COMMENT • link written 9 weeks ago by jordi.planells • 330
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