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arq5x / bedtools2

bedtools - the swiss army knife for genome arithmetic
MIT License
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shuffleBed -chrom not keeping chromosome distribution with -incl #96

Open abaresic opened 10 years ago

abaresic commented 10 years ago

I am trying to create a sample of single-base positions to test distribution of features for my dataset of SNPs. Also, this sample should be only within the coordinates of interest, i.e. some ~300 5-500kb regions, which I am providing with -incl.

Running it with -chrom, I would expect the output to have the same number of occurrences in chromosomes as the input file, it does not. Also, running it in a shell script repeatedly gives different distribution over chromosomes every time. Removing -incl solves the issue and each outfile has constant distribution across chromosomes, and the one matching the input file. Is that expected behaviour? Using v2.20.1 bedtools, CentOS 5.10...

Many thanks, Anja

arq5x commented 10 years ago

It looks like we don't support the -chrom and -incl options properly. I will look into fixing this for the next release

abaresic commented 10 years ago

Great, many thanks! Anja

On 11 July 2014 17:05, Aaron Quinlan notifications@github.com wrote:

It looks like we don't support the -chrom and -incl options properly. I will look into fixing this for the next release

— Reply to this email directly or view it on GitHub https://github.com/arq5x/bedtools2/issues/96#issuecomment-48749553.

Anja Baresic, Postdoctoral researcher, Computational Regulatory Genomics Group Institute of Clinical Science, Faculty of Medicine Imperial College London Hammersmith Hospital Campus Du Cane Road London W12 0NN